Biopython Tutorial and Cookbook

Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck,

Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczy
nski
Last Update 29 May 2014 (Biopython 1.64)

Contents
1 Introduction
1.1 What is Biopython? . . . . . . . . . . . .
1.2 What can I find in the Biopython package
1.3 Installing Biopython . . . . . . . . . . . .
1.4 Frequently Asked Questions (FAQ) . . . .

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

8
8
8
9
10

2 Quick Start What can you do with Biopython?

2.1 General overview of what Biopython provides . . . . . . .
2.2 Working with sequences . . . . . . . . . . . . . . . . . . .
2.3 A usage example . . . . . . . . . . . . . . . . . . . . . . .
2.4 Parsing sequence file formats . . . . . . . . . . . . . . . .
2.4.1 Simple FASTA parsing example . . . . . . . . . . .
2.4.2 Simple GenBank parsing example . . . . . . . . .
2.4.3 I love parsing please dont stop talking about it!
2.5 Connecting with biological databases . . . . . . . . . . . .
2.6 What to do next . . . . . . . . . . . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

13
13
13
14
15
15
16
16
16
17

3 Sequence objects
3.1 Sequences and Alphabets . . . . . . . . . . . . .
3.2 Sequences act like strings . . . . . . . . . . . . .
3.3 Slicing a sequence . . . . . . . . . . . . . . . . .
3.4 Turning Seq objects into strings . . . . . . . . . .
3.5 Concatenating or adding sequences . . . . . . . .
3.6 Changing case . . . . . . . . . . . . . . . . . . . .
3.7 Nucleotide sequences and (reverse) complements
3.8 Transcription . . . . . . . . . . . . . . . . . . . .
3.9 Translation . . . . . . . . . . . . . . . . . . . . .
3.10 Translation Tables . . . . . . . . . . . . . . . . .
3.11 Comparing Seq objects . . . . . . . . . . . . . . .
3.12 MutableSeq objects . . . . . . . . . . . . . . . . .
3.13 UnknownSeq objects . . . . . . . . . . . . . . . .
3.14 Working with strings directly . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.

18
18
19
20
21
21
23
23
24
25
27
28
29
30
31

4 Sequence annotation objects

4.1 The SeqRecord object . . . . . . . . . . . . .
4.2 Creating a SeqRecord . . . . . . . . . . . . .
4.2.1 SeqRecord objects from scratch . . . .
4.2.2 SeqRecord objects from FASTA files .
4.2.3 SeqRecord objects from GenBank files
4.3 Feature, location and position objects . . . .

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

33
33
34
34
35
36
37

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.
.
.

.
.
.
.

.
.
.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

37
38
41
42
42
42
45
47

5 Sequence Input/Output
5.1 Parsing or Reading Sequences . . . . . . . . . . . . . . . . . . . . .
5.1.1 Reading Sequence Files . . . . . . . . . . . . . . . . . . . .
5.1.2 Iterating over the records in a sequence file . . . . . . . . .
5.1.3 Getting a list of the records in a sequence file . . . . . . . .
5.1.4 Extracting data . . . . . . . . . . . . . . . . . . . . . . . . .
5.2 Parsing sequences from compressed files . . . . . . . . . . . . . . .
5.3 Parsing sequences from the net . . . . . . . . . . . . . . . . . . . .
5.3.1 Parsing GenBank records from the net . . . . . . . . . . . .
5.3.2 Parsing SwissProt sequences from the net . . . . . . . . . .
5.4 Sequence files as Dictionaries . . . . . . . . . . . . . . . . . . . . .
5.4.1 Sequence files as Dictionaries In memory . . . . . . . . .
5.4.2 Sequence files as Dictionaries Indexed files . . . . . . . . .
5.4.3 Sequence files as Dictionaries Database indexed files . . .
5.4.4 Indexing compressed files . . . . . . . . . . . . . . . . . . .
5.4.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.5 Writing Sequence Files . . . . . . . . . . . . . . . . . . . . . . . . .
5.5.1 Round trips . . . . . . . . . . . . . . . . . . . . . . . . . . .
5.5.2 Converting between sequence file formats . . . . . . . . . .
5.5.3 Converting a file of sequences to their reverse complements
5.5.4 Getting your SeqRecord objects as formatted strings . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

48
48
48
49
50
51
53
54
54
55
55
56
58
60
60
61
62
63
64
64
65

6 Multiple Sequence Alignment objects

6.1 Parsing or Reading Sequence Alignments . . . . . . . . . .
6.1.1 Single Alignments . . . . . . . . . . . . . . . . . . .
6.1.2 Multiple Alignments . . . . . . . . . . . . . . . . . .
6.1.3 Ambiguous Alignments . . . . . . . . . . . . . . . .
6.2 Writing Alignments . . . . . . . . . . . . . . . . . . . . . . .
6.2.1 Converting between sequence alignment file formats
6.2.2 Getting your alignment objects as formatted strings
6.3 Manipulating Alignments . . . . . . . . . . . . . . . . . . .
6.3.1 Slicing alignments . . . . . . . . . . . . . . . . . . .
6.3.2 Alignments as arrays . . . . . . . . . . . . . . . . . .
6.4 Alignment Tools . . . . . . . . . . . . . . . . . . . . . . . .
6.4.1 ClustalW . . . . . . . . . . . . . . . . . . . . . . . .
6.4.2 MUSCLE . . . . . . . . . . . . . . . . . . . . . . . .
6.4.3 MUSCLE using stdout . . . . . . . . . . . . . . . . .
6.4.4 MUSCLE using stdin and stdout . . . . . . . . . . .
6.4.5 EMBOSS needle and water . . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

67
67
68
70
72
74
75
77
78
78
81
81
82
83
84
85
87

4.4
4.5
4.6
4.7
4.8

4.3.1 SeqFeature objects . . . . . . . . . . . . . .

4.3.2 Positions and locations . . . . . . . . . . . .
4.3.3 Sequence described by a feature or location
References . . . . . . . . . . . . . . . . . . . . . . .
The format method . . . . . . . . . . . . . . . . . .
Slicing a SeqRecord . . . . . . . . . . . . . . . . .
Adding SeqRecord objects . . . . . . . . . . . . . .
Reverse-complementing SeqRecord objects . . . . .

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

7 BLAST
7.1 Running BLAST over the Internet . . . . . . . . . . . . . .
7.2 Running BLAST locally . . . . . . . . . . . . . . . . . . . .
7.2.1 Introduction . . . . . . . . . . . . . . . . . . . . . .
7.2.2 Standalone NCBI BLAST+ . . . . . . . . . . . . . .
7.2.3 Other versions of BLAST . . . . . . . . . . . . . . .
7.3 Parsing BLAST output . . . . . . . . . . . . . . . . . . . .
7.4 The BLAST record class . . . . . . . . . . . . . . . . . . . .
7.5 Deprecated BLAST parsers . . . . . . . . . . . . . . . . . .
7.5.1 Parsing plain-text BLAST output . . . . . . . . . .
7.5.2 Parsing a plain-text BLAST file full of BLAST runs
7.5.3 Finding a bad record somewhere in a huge plain-text
7.6 Dealing with PSI-BLAST . . . . . . . . . . . . . . . . . . .
7.7 Dealing with RPS-BLAST . . . . . . . . . . . . . . . . . . .

. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
. . . . . . .
BLAST file
. . . . . . .
. . . . . . .

8 BLAST and other sequence search tools (experimental code)

8.1 The SearchIO object model . . . . . . . . . . . . . . . . . . . . .
8.1.1 QueryResult . . . . . . . . . . . . . . . . . . . . . . . . .
8.1.2 Hit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
8.1.3 HSP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
8.1.4 HSPFragment . . . . . . . . . . . . . . . . . . . . . . . . .
8.2 A note about standards and conventions . . . . . . . . . . . . . .
8.3 Reading search output files . . . . . . . . . . . . . . . . . . . . .
8.4 Dealing with large search output files with indexing . . . . . . .
8.5 Writing and converting search output files . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.

89
. 89
. 91
. 91
. 91
. 92
. 92
. 94
. 95
. 95
. 98
. 99
. 100
. 100

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

101
102
102
107
110
113
114
115
115
116

9 Accessing NCBIs Entrez databases

9.1 Entrez Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9.2 EInfo: Obtaining information about the Entrez databases . . . . . . .
9.3 ESearch: Searching the Entrez databases . . . . . . . . . . . . . . . . .
9.4 EPost: Uploading a list of identifiers . . . . . . . . . . . . . . . . . . .
9.5 ESummary: Retrieving summaries from primary IDs . . . . . . . . . .
9.6 EFetch: Downloading full records from Entrez . . . . . . . . . . . . . .
9.7 ELink: Searching for related items in NCBI Entrez . . . . . . . . . . .
9.8 EGQuery: Global Query - counts for search terms . . . . . . . . . . .
9.9 ESpell: Obtaining spelling suggestions . . . . . . . . . . . . . . . . . .
9.10 Parsing huge Entrez XML files . . . . . . . . . . . . . . . . . . . . . .
9.11 Handling errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9.12 Specialized parsers . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9.12.1 Parsing Medline records . . . . . . . . . . . . . . . . . . . . . .
9.12.2 Parsing GEO records . . . . . . . . . . . . . . . . . . . . . . . .
9.12.3 Parsing UniGene records . . . . . . . . . . . . . . . . . . . . . .
9.13 Using a proxy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9.14 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9.14.1 PubMed and Medline . . . . . . . . . . . . . . . . . . . . . . .
9.14.2 Searching, downloading, and parsing Entrez Nucleotide records
9.14.3 Searching, downloading, and parsing GenBank records . . . . .
9.14.4 Finding the lineage of an organism . . . . . . . . . . . . . . . .
9.15 Using the history and WebEnv . . . . . . . . . . . . . . . . . . . . . .
9.15.1 Searching for and downloading sequences using the history . .
9.15.2 Searching for and downloading abstracts using the history . . .
9.15.3 Searching for citations . . . . . . . . . . . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

118
119
120
122
122
123
123
126
128
128
128
129
131
132
134
134
136
136
136
137
139
140
141
141
142
143

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

10 Swiss-Prot and ExPASy

10.1 Parsing Swiss-Prot files . . . . . . . . . . . . . . . . . . . . .
10.1.1 Parsing Swiss-Prot records . . . . . . . . . . . . . . .
10.1.2 Parsing the Swiss-Prot keyword and category list . . .
10.2 Parsing Prosite records . . . . . . . . . . . . . . . . . . . . . .
10.3 Parsing Prosite documentation records . . . . . . . . . . . . .
10.4 Parsing Enzyme records . . . . . . . . . . . . . . . . . . . . .
10.5 Accessing the ExPASy server . . . . . . . . . . . . . . . . . .
10.5.1 Retrieving a Swiss-Prot record . . . . . . . . . . . . .
10.5.2 Searching Swiss-Prot . . . . . . . . . . . . . . . . . . .
10.5.3 Retrieving Prosite and Prosite documentation records
10.6 Scanning the Prosite database . . . . . . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

144
144
144
146
147
148
148
150
150
151
151
152

11 Going 3D: The PDB module

11.1 Reading and writing crystal structure files . . . . . . . . . . . . . . . . . . .
11.1.1 Reading a PDB file . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.1.2 Reading an mmCIF file . . . . . . . . . . . . . . . . . . . . . . . . .
11.1.3 Reading files in the PDB XML format . . . . . . . . . . . . . . . . .
11.1.4 Writing PDB files . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.2 Structure representation . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.2.1 Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.2.2 Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.2.3 Chain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.2.4 Residue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.2.5 Atom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.2.6 Extracting a specific Atom/Residue/Chain/Model from a Structure .
11.3 Disorder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.3.1 General approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.3.2 Disordered atoms . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.3.3 Disordered residues . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.4 Hetero residues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.4.1 Associated problems . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.4.2 Water residues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.4.3 Other hetero residues . . . . . . . . . . . . . . . . . . . . . . . . . .
11.5 Navigating through a Structure object . . . . . . . . . . . . . . . . . . . . .
11.6 Analyzing structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.6.1 Measuring distances . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.6.2 Measuring angles . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.6.3 Measuring torsion angles . . . . . . . . . . . . . . . . . . . . . . . . .
11.6.4 Determining atom-atom contacts . . . . . . . . . . . . . . . . . . . .
11.6.5 Superimposing two structures . . . . . . . . . . . . . . . . . . . . . .
11.6.6 Mapping the residues of two related structures onto each other . . .
11.6.7 Calculating the Half Sphere Exposure . . . . . . . . . . . . . . . . .
11.6.8 Determining the secondary structure . . . . . . . . . . . . . . . . . .
11.6.9 Calculating the residue depth . . . . . . . . . . . . . . . . . . . . . .
11.7 Common problems in PDB files . . . . . . . . . . . . . . . . . . . . . . . . .
11.7.1 Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.7.2 Automatic correction . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.7.3 Fatal errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11.8 Accessing the Protein Data Bank . . . . . . . . . . . . . . . . . . . . . . . .
11.8.1 Downloading structures from the Protein Data Bank . . . . . . . . .
11.8.2 Downloading the entire PDB . . . . . . . . . . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

154
154
154
155
155
155
156
158
159
159
159
160
161
162
162
162
162
163
163
163
163
163
166
166
166
166
167
167
167
167
168
168
169
169
170
170
171
171
171

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.

11.8.3 Keeping a local copy of the PDB up to date

11.9 General questions . . . . . . . . . . . . . . . . . . .
11.9.1 How well tested is Bio.PDB? . . . . . . . .
11.9.2 How fast is it? . . . . . . . . . . . . . . . .
11.9.3 Is there support for molecular graphics? . .
11.9.4 Whos using Bio.PDB? . . . . . . . . . . . .
12 Bio.PopGen: Population genetics
12.1 GenePop . . . . . . . . . . . . . .
12.2 Coalescent simulation . . . . . .
12.2.1 Creating scenarios . . . .
12.2.2 Running Fastsimcoal2 . .
12.3 Other applications . . . . . . . .
12.3.1 FDist: Detecting selection
12.4 Future Developments . . . . . . .

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.

171
172
172
172
172
172

. . . . . . . . . . . . . . .
. . . . . . . . . . . . . . .
. . . . . . . . . . . . . . .
. . . . . . . . . . . . . . .
. . . . . . . . . . . . . . .
and molecular adaptation
. . . . . . . . . . . . . . .

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

173
173
175
175
177
178
178
181

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

182
182
183
186
187
191
191
193
193
194
194
195
195

. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
Scoring Matrix
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .
. . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

197
197
197
199
200
200
206
209
212
213
214
215
215
216
216
217
220
221
221
222
223

13 Phylogenetics with Bio.Phylo

13.1 Demo: Whats in a Tree? . . . . . . .
13.1.1 Coloring branches within a tree
13.2 I/O functions . . . . . . . . . . . . . .
13.3 View and export trees . . . . . . . . .
13.4 Using Tree and Clade objects . . . . .
13.4.1 Search and traversal methods .
13.4.2 Information methods . . . . . .
13.4.3 Modification methods . . . . .
13.4.4 Features of PhyloXML trees . .
13.5 Running external applications . . . . .
13.6 PAML integration . . . . . . . . . . .
13.7 Future plans . . . . . . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

14 Sequence motif analysis using Bio.motifs

14.1 Motif objects . . . . . . . . . . . . . . . . . . . . . .
14.1.1 Creating a motif from instances . . . . . . . .
14.1.2 Creating a sequence logo . . . . . . . . . . . .
14.2 Reading motifs . . . . . . . . . . . . . . . . . . . . .
14.2.1 JASPAR . . . . . . . . . . . . . . . . . . . .
14.2.2 MEME . . . . . . . . . . . . . . . . . . . . .
14.2.3 TRANSFAC . . . . . . . . . . . . . . . . . .
14.3 Writing motifs . . . . . . . . . . . . . . . . . . . . .
14.4 Position-Weight Matrices . . . . . . . . . . . . . . .
14.5 Position-Specific Scoring Matrices . . . . . . . . . . .
14.6 Searching for instances . . . . . . . . . . . . . . . . .
14.6.1 Searching for exact matches . . . . . . . . . .
14.6.2 Searching for matches using the PSSM score
14.6.3 Selecting a score threshold . . . . . . . . . . .
14.7 Each motif object has an associated Position-Specific
14.8 Comparing motifs . . . . . . . . . . . . . . . . . . .
14.9 De novo motif finding . . . . . . . . . . . . . . . . .
14.9.1 MEME . . . . . . . . . . . . . . . . . . . . .
14.9.2 AlignAce . . . . . . . . . . . . . . . . . . . .
14.10Useful links . . . . . . . . . . . . . . . . . . . . . . .

.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

15 Cluster analysis
15.1 Distance functions . . . . . . . . . .
15.2 Calculating cluster properties . . . .
15.3 Partitioning algorithms . . . . . . .
15.4 Hierarchical clustering . . . . . . . .
15.5 Self-Organizing Maps . . . . . . . . .
15.6 Principal Component Analysis . . .
15.7 Handling Cluster/TreeView-type files
15.8 Example calculation . . . . . . . . .
15.9 Auxiliary functions . . . . . . . . . .

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.

224
225
228
230
233
237
239
240
245
245

16 Supervised learning methods

16.1 The Logistic Regression Model . . . . . . . . . . . . . . . . .
16.1.1 Background and Purpose . . . . . . . . . . . . . . . .
16.1.2 Training the logistic regression model . . . . . . . . .
16.1.3 Using the logistic regression model for classification .
16.1.4 Logistic Regression, Linear Discriminant Analysis, and
16.2 k-Nearest Neighbors . . . . . . . . . . . . . . . . . . . . . . .
16.2.1 Background and purpose . . . . . . . . . . . . . . . .
16.2.2 Initializing a k-nearest neighbors model . . . . . . . .
16.2.3 Using a k-nearest neighbors model for classification . .
16.3 Nave Bayes . . . . . . . . . . . . . . . . . . . . . . . . . . . .
16.4 Maximum Entropy . . . . . . . . . . . . . . . . . . . . . . . .
16.5 Markov Models . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . .
. . . . .
. . . . .
. . . . .
Support
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .

. . . .
. . . .
. . . .
. . . .
Vector
. . . .
. . . .
. . . .
. . . .
. . . .
. . . .
. . . .

. . . . . .
. . . . . .
. . . . . .
. . . . . .
Machines
. . . . . .
. . . . . .
. . . . . .
. . . . . .
. . . . . .
. . . . . .
. . . . . .

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.

246
246
246
247
249
251
251
251
252
252
254
254
254

17 Graphics including GenomeDiagram

17.1 GenomeDiagram . . . . . . . . . . . . . . . . . . .
17.1.1 Introduction . . . . . . . . . . . . . . . . .
17.1.2 Diagrams, tracks, feature-sets and features
17.1.3 A top down example . . . . . . . . . . . . .
17.1.4 A bottom up example . . . . . . . . . . . .
17.1.5 Features without a SeqFeature . . . . . . .
17.1.6 Feature captions . . . . . . . . . . . . . . .
17.1.7 Feature sigils . . . . . . . . . . . . . . . . .
17.1.8 Arrow sigils . . . . . . . . . . . . . . . . . .
17.1.9 A nice example . . . . . . . . . . . . . . . .
17.1.10 Multiple tracks . . . . . . . . . . . . . . . .
17.1.11 Cross-Links between tracks . . . . . . . . .
17.1.12 Further options . . . . . . . . . . . . . . . .
17.1.13 Converting old code . . . . . . . . . . . . .
17.2 Chromosomes . . . . . . . . . . . . . . . . . . . . .
17.2.1 Simple Chromosomes . . . . . . . . . . . .
17.2.2 Annotated Chromosomes . . . . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

255
255
255
255
256
258
258
259
261
261
265
266
269
273
274
274
274
277

18 Cookbook Cool things to do with it

18.1 Working with sequence files . . . . . . . . . . . . . . . .
18.1.1 Filtering a sequence file . . . . . . . . . . . . . .
18.1.2 Producing randomised genomes . . . . . . . . . .
18.1.3 Translating a FASTA file of CDS entries . . . . .
18.1.4 Making the sequences in a FASTA file upper case
18.1.5 Sorting a sequence file . . . . . . . . . . . . . . .
18.1.6 Simple quality filtering for FASTQ files . . . . .

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

279
279
279
280
281
282
282
283

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

18.2

18.3

18.4

18.5

18.1.7 Trimming off primer sequences . . . . . . . . . . . . . . .

18.1.8 Trimming off adaptor sequences . . . . . . . . . . . . . . .
18.1.9 Converting FASTQ files . . . . . . . . . . . . . . . . . . .
18.1.10 Converting FASTA and QUAL files into FASTQ files . . .
18.1.11 Indexing a FASTQ file . . . . . . . . . . . . . . . . . . . .
18.1.12 Converting SFF files . . . . . . . . . . . . . . . . . . . . .
18.1.13 Identifying open reading frames . . . . . . . . . . . . . . .
Sequence parsing plus simple plots . . . . . . . . . . . . . . . . .
18.2.1 Histogram of sequence lengths . . . . . . . . . . . . . . .
18.2.2 Plot of sequence GC% . . . . . . . . . . . . . . . . . . . .
18.2.3 Nucleotide dot plots . . . . . . . . . . . . . . . . . . . . .
18.2.4 Plotting the quality scores of sequencing read data . . . .
Dealing with alignments . . . . . . . . . . . . . . . . . . . . . . .
18.3.1 Calculating summary information . . . . . . . . . . . . .
18.3.2 Calculating a quick consensus sequence . . . . . . . . . .
18.3.3 Position Specific Score Matrices . . . . . . . . . . . . . . .
18.3.4 Information Content . . . . . . . . . . . . . . . . . . . . .
Substitution Matrices . . . . . . . . . . . . . . . . . . . . . . . .
18.4.1 Using common substitution matrices . . . . . . . . . . . .
18.4.2 Creating your own substitution matrix from an alignment
BioSQL storing sequences in a relational database . . . . . . .

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.

284
285
286
288
288
289
290
292
292
293
294
296
297
298
298
299
300
302
302
302
303

19 The Biopython testing framework

19.1 Running the tests . . . . . . . . . . . . .
19.2 Writing tests . . . . . . . . . . . . . . .
19.2.1 Writing a print-and-compare test
19.2.2 Writing a unittest-based test . .
19.3 Writing doctests . . . . . . . . . . . . .

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

.
.
.
.
.

304
304
305
306
307
310

20 Advanced
20.1 Parser Design . . . . .
20.2 Substitution Matrices
20.2.1 SubsMat . . . .
20.2.2 FreqTable . . .

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

311
311
311
311
314

21 Where to go from here contributing to Biopython

21.1 Bug Reports + Feature Requests . . . . . . . . . . . .
21.2 Mailing lists and helping newcomers . . . . . . . . . .
21.3 Contributing Documentation . . . . . . . . . . . . . .
21.4 Contributing cookbook examples . . . . . . . . . . . .
21.5 Maintaining a distribution for a platform . . . . . . .
21.6 Contributing Unit Tests . . . . . . . . . . . . . . . . .
21.7 Contributing Code . . . . . . . . . . . . . . . . . . . .

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

.
.
.
.
.
.
.

316
316
316
316
316
317
317
318

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

.
.
.
.

22 Appendix: Useful stuff about Python

319
22.1 What the heck is a handle? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319
22.1.1 Creating a handle from a string . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320

Chapter 1

Introduction
1.1

What is Biopython?

The Biopython Project is an international association of developers of freely available Python (http://www.
python.org) tools for computational molecular biology. Python is an object oriented, interpreted, flexible
language that is becoming increasingly popular for scientific computing. Python is easy to learn, has a very
clear syntax and can easily be extended with modules written in C, C++ or FORTRAN.
The Biopython web site (http://www.biopython.org) provides an online resource for modules, scripts,
and web links for developers of Python-based software for bioinformatics use and research. Basically, the
goal of Biopython is to make it as easy as possible to use Python for bioinformatics by creating high-quality,
reusable modules and classes. Biopython features include parsers for various Bioinformatics file formats
(BLAST, Clustalw, FASTA, Genbank,...), access to online services (NCBI, Expasy,...), interfaces to common
and not-so-common programs (Clustalw, DSSP, MSMS...), a standard sequence class, various clustering
modules, a KD tree data structure etc. and even documentation.
Basically, we just like to program in Python and want to make it as easy as possible to use Python for
bioinformatics by creating high-quality, reusable modules and scripts.

1.2

What can I find in the Biopython package

The main Biopython releases have lots of functionality, including:

The ability to parse bioinformatics files into Python utilizable data structures, including support for
the following formats:
Blast output both from standalone and WWW Blast
Clustalw
FASTA
GenBank
PubMed and Medline
ExPASy files, like Enzyme and Prosite
SCOP, including dom and lin files
UniGene
SwissProt
Files in the supported formats can be iterated over record by record or indexed and accessed via a
Dictionary interface.
8

 Code to deal with popular on-line bioinformatics destinations such as:

NCBI Blast, Entrez and PubMed services
ExPASy Swiss-Prot and Prosite entries, as well as Prosite searches
Interfaces to common bioinformatics programs such as:
Standalone Blast from NCBI
Clustalw alignment program
EMBOSS command line tools
A standard sequence class that deals with sequences, ids on sequences, and sequence features.
Tools for performing common operations on sequences, such as translation, transcription and weight
calculations.
Code to perform classification of data using k Nearest Neighbors, Naive Bayes or Support Vector
Machines.
Code for dealing with alignments, including a standard way to create and deal with substitution
matrices.
Code making it easy to split up parallelizable tasks into separate processes.
GUI-based programs to do basic sequence manipulations, translations, BLASTing, etc.
Extensive documentation and help with using the modules, including this file, on-line wiki documentation, the web site, and the mailing list.
Integration with BioSQL, a sequence database schema also supported by the BioPerl and BioJava
projects.
We hope this gives you plenty of reasons to download and start using Biopython!

1.3

Installing Biopython

All of the installation information for Biopython was separated from this document to make it easier to keep
updated.
The short version is go to our downloads page (http://biopython.org/wiki/Download), download and
install the listed dependencies, then download and install Biopython. Biopython runs on many platforms
(Windows, Mac, and on the various flavors of Linux and Unix). For Windows we provide pre-compiled clickand-run installers, while for Unix and other operating systems you must install from source as described in
the included README file. This is usually as simple as the standard commands:
python setup.py build
python setup.py test
sudo python setup.py install
(You can in fact skip the build and test, and go straight to the install but its better to make sure everything
seems to be working.)
The longer version of our installation instructions covers installation of Python, Biopython dependencies
and Biopython itself. It is available in PDF (http://biopython.org/DIST/docs/install/Installation.
pdf) and HTML formats (http://biopython.org/DIST/docs/install/Installation.html).

1.4

Frequently Asked Questions (FAQ)

1. How do I cite Biopython in a scientific publication?

Please cite our application note [1, Cock et al., 2009] as the main Biopython reference. In addition,
please cite any publications from the following list if appropriate, in particular as a reference for specific
modules within Biopython (more information can be found on our website):
For the official project announcement: [13, Chapman and Chang, 2000];
For Bio.PDB: [18, Hamelryck and Manderick, 2003];
For Bio.Cluster: [14, De Hoon et al., 2004];
For Bio.Graphics.GenomeDiagram: [2, Pritchard et al., 2006];
For Bio.Phylo and Bio.Phylo.PAML: [9, Talevich et al., 2012];
For the FASTQ file format as supported in Biopython, BioPerl, BioRuby, BioJava, and EMBOSS:
[7, Cock et al., 2010].
2. How should I capitalize Biopython? Is BioPython OK?
The correct capitalization is Biopython, not BioPython (even though that would have matched
BioPerl, BioJava and BioRuby).
3. What is going wrong with my print commands?
This tutorial now uses the Python 3 style print function. As of Biopython 1.62, we support both
Python 2 and Python 3. The most obvious language difference is the print statement in Python 2
became a print function in Python 3.
For example, this will only work under Python 2:
>>> print "Hello World!"
Hello World!
If you try that on Python 3 youll get a SyntaxError. Under Python 3 you must write:
>>> print("Hello World!")
Hello World!
Surprisingly that will also work on Python 2 but only for simple examples printing one thing. In
general you need to add this magic line to the start of your Python scripts to use the print function
under Python 2.6 and 2.7:
from __future__ import print_function
If you forget to add this magic import, under Python 2 youll see extra brackets produced by trying
to use the print function when Python 2 is interpreting it as a print statement and a tuple.
4. How do I find out what version of Biopython I have installed?
Use this:
>>> import Bio
>>> print(Bio.__version__)
...

10

If the import Bio line fails, Biopython is not installed. If the second line fails, your version is very
out of date. If the version string ends with a plus, you dont have an official release, but a snapshot of
the in development code.
5. Where is the latest version of this document?
If you download a Biopython source code archive, it will include the relevant version in both HTML
and PDF formats. The latest published version of this document (updated at each release) is online:
http://biopython.org/DIST/docs/tutorial/Tutorial.html
http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
If you are using the very latest unreleased code from our repository you can find copies of the in-progress
tutorial here:
http://biopython.org/DIST/docs/tutorial/Tutorial-dev.html
http://biopython.org/DIST/docs/tutorial/Tutorial-dev.pdf
6. Why is the Seq object missing the upper & lower methods described in this Tutorial?
You need Biopython 1.53 or later. Alternatively, use str(my_seq).upper() to get an upper case
string. If you need a Seq object, try Seq(str(my_seq).upper()) but be careful about blindly re-using
the same alphabet.
7. Why doesnt the Seq object translation method support the cds option described in this Tutorial?
You need Biopython 1.51 or later.
8. What file formats do Bio.SeqIO and Bio.AlignIO read and write?
Check the built in docstrings (from Bio import SeqIO, then help(SeqIO)), or see http://biopython.
org/wiki/SeqIO and http://biopython.org/wiki/AlignIO on the wiki for the latest listing.
9. Why wont the Bio.SeqIO and Bio.AlignIO functions parse, read and write take filenames? They
insist on handles!
You need Biopython 1.54 or later, or just use handles explicitly (see Section 22.1). It is especially
important to remember to close output handles explicitly after writing your data.
10. Why wont the Bio.SeqIO.write() and Bio.AlignIO.write() functions accept a single record or
alignment? They insist on a list or iterator!
You need Biopython 1.54 or later, or just wrap the item with [...] to create a list of one element.
11. Why doesnt str(...) give me the full sequence of a Seq object?
You need Biopython 1.45 or later.
12. Why doesnt Bio.Blast work with the latest plain text NCBI blast output?
The NCBI keep tweaking the plain text output from the BLAST tools, and keeping our parser up
to date is/was an ongoing struggle. If you arent using the latest version of Biopython, you could
try upgrading. However, we (and the NCBI) recommend you use the XML output instead, which is
designed to be read by a computer program.
13. Why doesnt Bio.Entrez.parse() work? The module imports fine but there is no parse function!
You need Biopython 1.52 or later.
14. Why has my script using Bio.Entrez.efetch() stopped working?
This could be due to NCBI changes in February 2012 introducing EFetch 2.0. First, they changed
the default return modes - you probably want to add retmode="text" to your call. Second, they are
now stricter about how to provide a list of IDs Biopython 1.59 onwards turns a list into a comma
separated string automatically.

11

15. Why doesnt Bio.Blast.NCBIWWW.qblast() give the same results as the NCBI BLAST website?
You need to specify the same options the NCBI often adjust the default settings on the website, and
they do not match the QBLAST defaults anymore. Check things like the gap penalties and expectation
threshold.
16. Why doesnt Bio.Blast.NCBIXML.read() work? The module imports but there is no read function!
You need Biopython 1.50 or later. Or, use next(Bio.Blast.NCBIXML.parse(...)) instead.
17. Why doesnt my SeqRecord object have a letter_annotations attribute?
Per-letter-annotation support was added in Biopython 1.50.
18. Why cant I slice my SeqRecord to get a sub-record?
You need Biopython 1.50 or later.
19. Why cant I add SeqRecord objects together?
You need Biopython 1.53 or later.
20. Why doesnt Bio.SeqIO.convert() or Bio.AlignIO.convert() work? The modules import fine but
there is no convert function!
You need Biopython 1.52 or later. Alternatively, combine the parse and write functions as described
in this tutorial (see Sections 5.5.2 and 6.2.1).
21. Why doesnt Bio.SeqIO.index() work? The module imports fine but there is no index function!
You need Biopython 1.52 or later.
22. Why doesnt Bio.SeqIO.index_db() work? The module imports fine but there is no index db function!
You need Biopython 1.57 or later (and a Python with SQLite3 support).
23. Where is the MultipleSeqAlignment object? The Bio.Align module imports fine but this class isnt
there!
You need Biopython 1.54 or later. Alternatively, the older Bio.Align.Generic.Alignment class supports some of its functionality, but using this is now discouraged.
24. Why cant I run command line tools directly from the application wrappers?
You need Biopython 1.55 or later. Alternatively, use the Python subprocess module directly.
25. I looked in a directory for code, but I couldnt find the code that does something. Wheres it hidden?
One thing to know is that we put code in __init__.py files. If you are not used to looking for code
in this file this can be confusing. The reason we do this is to make the imports easier for users. For
instance, instead of having to do a repetitive import like from Bio.GenBank import GenBank, you
can just use from Bio import GenBank.
26. Why does the code from CVS seem out of date?
In late September 2009, just after the release of Biopython 1.52, we switched from using CVS to git,
a distributed version control system. The old CVS server will remain available as a static and read
only backup, but if you want to grab the latest code, youll need to use git instead. See our website
for more details.
For more general questions, the Python FAQ pages http://www.python.org/doc/faq/ may be useful.

12

Chapter 2

Quick Start What can you do with

Biopython?
This section is designed to get you started quickly with Biopython, and to give a general overview of what is
available and how to use it. All of the examples in this section assume that you have some general working
knowledge of Python, and that you have successfully installed Biopython on your system. If you think you
need to brush up on your Python, the main Python web site provides quite a bit of free documentation to
get started with (http://www.python.org/doc/).
Since much biological work on the computer involves connecting with databases on the internet, some of
the examples will also require a working internet connection in order to run.
Now that that is all out of the way, lets get into what we can do with Biopython.

2.1

General overview of what Biopython provides

As mentioned in the introduction, Biopython is a set of libraries to provide the ability to deal with things
of interest to biologists working on the computer. In general this means that you will need to have at
least some programming experience (in Python, of course!) or at least an interest in learning to program.
Biopythons job is to make your job easier as a programmer by supplying reusable libraries so that you
can focus on answering your specific question of interest, instead of focusing on the internals of parsing a
particular file format (of course, if you want to help by writing a parser that doesnt exist and contributing
it to Biopython, please go ahead!). So Biopythons job is to make you happy!
One thing to note about Biopython is that it often provides multiple ways of doing the same thing.
Things have improved in recent releases, but this can still be frustrating as in Python there should ideally
be one right way to do something. However, this can also be a real benefit because it gives you lots of
flexibility and control over the libraries. The tutorial helps to show you the common or easy ways to do
things so that you can just make things work. To learn more about the alternative possibilities, look in the
Cookbook (Chapter 18, this has some cools tricks and tips), the Advanced section (Chapter 20), the built
in docstrings (via the Python help command, or the API documentation) or ultimately the code itself.

2.2

Working with sequences

Disputably (of course!), the central object in bioinformatics is the sequence. Thus, well start with a quick
introduction to the Biopython mechanisms for dealing with sequences, the Seq object, which well discuss in
more detail in Chapter 3.
Most of the time when we think about sequences we have in my mind a string of letters like AGTACACTGGT.
You can create such Seq object with this sequence as follows - the >>> represents the Python prompt

13

followed by what you would type in:

>>> from Bio.Seq import Seq
>>> my_seq = Seq("AGTACACTGGT")
>>> my_seq
Seq(AGTACACTGGT, Alphabet())
>>> print(my_seq)
AGTACACTGGT
>>> my_seq.alphabet
Alphabet()
What we have here is a sequence object with a generic alphabet - reflecting the fact we have not specified if this is a DNA or protein sequence (okay, a protein with a lot of Alanines, Glycines, Cysteines and
Threonines!). Well talk more about alphabets in Chapter 3.
In addition to having an alphabet, the Seq object differs from the Python string in the methods it
supports. You cant do this with a plain string:
>>> my_seq
Seq(AGTACACTGGT, Alphabet())
>>> my_seq.complement()
Seq(TCATGTGACCA, Alphabet())
>>> my_seq.reverse_complement()
Seq(ACCAGTGTACT, Alphabet())
The next most important class is the SeqRecord or Sequence Record. This holds a sequence (as a Seq
object) with additional annotation including an identifier, name and description. The Bio.SeqIO module
for reading and writing sequence file formats works with SeqRecord objects, which will be introduced below
and covered in more detail by Chapter 5.
This covers the basic features and uses of the Biopython sequence class. Now that youve got some idea
of what it is like to interact with the Biopython libraries, its time to delve into the fun, fun world of dealing
with biological file formats!

2.3

A usage example

Before we jump right into parsers and everything else to do with Biopython, lets set up an example to
motivate everything we do and make life more interesting. After all, if there wasnt any biology in this
tutorial, why would you want you read it?
Since I love plants, I think were just going to have to have a plant based example (sorry to all the fans
of other organisms out there!). Having just completed a recent trip to our local greenhouse, weve suddenly
developed an incredible obsession with Lady Slipper Orchids (if you wonder why, have a look at some Lady
Slipper Orchids photos on Flickr, or try a Google Image Search).
Of course, orchids are not only beautiful to look at, they are also extremely interesting for people studying
evolution and systematics. So lets suppose were thinking about writing a funding proposal to do a molecular
study of Lady Slipper evolution, and would like to see what kind of research has already been done and how
we can add to that.
After a little bit of reading up we discover that the Lady Slipper Orchids are in the Orchidaceae family and
the Cypripedioideae sub-family and are made up of 5 genera: Cypripedium, Paphiopedilum, Phragmipedium,
Selenipedium and Mexipedium.
That gives us enough to get started delving for more information. So, lets look at how the Biopython
tools can help us. Well start with sequence parsing in Section 2.4, but the orchids will be back later on as
well - for example well search PubMed for papers about orchids and extract sequence data from GenBank in
Chapter 9, extract data from Swiss-Prot from certain orchid proteins in Chapter 10, and work with ClustalW
multiple sequence alignments of orchid proteins in Section 6.4.1.
14

2.4

Parsing sequence file formats

A large part of much bioinformatics work involves dealing with the many types of file formats designed to
hold biological data. These files are loaded with interesting biological data, and a special challenge is parsing
these files into a format so that you can manipulate them with some kind of programming language. However
the task of parsing these files can be frustrated by the fact that the formats can change quite regularly, and
that formats may contain small subtleties which can break even the most well designed parsers.
We are now going to briefly introduce the Bio.SeqIO module you can find out more in Chapter 5. Well
start with an online search for our friends, the lady slipper orchids. To keep this introduction simple, were
just using the NCBI website by hand. Lets just take a look through the nucleotide databases at NCBI,
using an Entrez online search (http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Nucleotide)
for everything mentioning the text Cypripedioideae (this is the subfamily of lady slipper orchids).
When this tutorial was originally written, this search gave us only 94 hits, which we saved as a FASTA
formatted text file and as a GenBank formatted text file (files ls orchid.fasta and ls orchid.gbk, also
included with the Biopython source code under docs/tutorial/examples/).
If you run the search today, youll get hundreds of results! When following the tutorial, if you want to
see the same list of genes, just download the two files above or copy them from docs/examples/ in the
Biopython source code. In Section 2.5 we will look at how to do a search like this from within Python.

2.4.1

Simple FASTA parsing example

If you open the lady slipper orchids FASTA file ls orchid.fasta in your favourite text editor, youll see
that the file starts like this:
>gi|2765658|emb|Z78533.1|CIZ78533 C.irapeanum 5.8S rRNA gene and ITS1 and ITS2 DNA
CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGGAATAAACGATCGAGTG
AATCCGGAGGACCGGTGTACTCAGCTCACCGGGGGCATTGCTCCCGTGGTGACCCTGATTTGTTGTTGGG
...
It contains 94 records, each has a line starting with > (greater-than symbol) followed by the sequence
on one or more lines. Now try this in Python:
from Bio import SeqIO
for seq_record in SeqIO.parse("ls_orchid.fasta", "fasta"):
print(seq_record.id)
print(repr(seq_record.seq))
print(len(seq_record))
You should get something like this on your screen:
gi|2765658|emb|Z78533.1|CIZ78533
Seq(CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG...CGC, SingleLetterAlphabet())
740
...
gi|2765564|emb|Z78439.1|PBZ78439
Seq(CATTGTTGAGATCACATAATAATTGATCGAGTTAATCTGGAGGATCTGTTTACT...GCC, SingleLetterAlphabet())
592
Notice that the FASTA format does not specify the alphabet, so Bio.SeqIO has defaulted to the rather
generic SingleLetterAlphabet() rather than something DNA specific.

15

2.4.2

Simple GenBank parsing example

Now lets load the GenBank file ls orchid.gbk instead - notice that the code to do this is almost identical
to the snippet used above for the FASTA file - the only difference is we change the filename and the format
string:
from Bio import SeqIO
for seq_record in SeqIO.parse("ls_orchid.gbk", "genbank"):
print(seq_record.id)
print(repr(seq_record.seq))
print(len(seq_record))
This should give:
Z78533.1
Seq(CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG...CGC, IUPACAmbiguousDNA())
740
...
Z78439.1
Seq(CATTGTTGAGATCACATAATAATTGATCGAGTTAATCTGGAGGATCTGTTTACT...GCC, IUPACAmbiguousDNA())
592
This time Bio.SeqIO has been able to choose a sensible alphabet, IUPAC Ambiguous DNA. Youll also
notice that a shorter string has been used as the seq_record.id in this case.

2.4.3

I love parsing please dont stop talking about it!

Biopython has a lot of parsers, and each has its own little special niches based on the sequence format it is
parsing and all of that. Chapter 5 covers Bio.SeqIO in more detail, while Chapter 6 introduces Bio.AlignIO
for sequence alignments.
While the most popular file formats have parsers integrated into Bio.SeqIO and/or Bio.AlignIO, for
some of the rarer and unloved file formats there is either no parser at all, or an old parser which has
not been linked in yet. Please also check the wiki pages http://biopython.org/wiki/SeqIO and http:
//biopython.org/wiki/AlignIO for the latest information, or ask on the mailing list. The wiki pages
should include an up to date list of supported file types, and some additional examples.
The next place to look for information about specific parsers and how to do cool things with them is in
the Cookbook (Chapter 18 of this Tutorial). If you dont find the information you are looking for, please
consider helping out your poor overworked documentors and submitting a cookbook entry about it! (once
you figure out how to do it, that is!)

2.5

Connecting with biological databases

One of the very common things that you need to do in bioinformatics is extract information from biological
databases. It can be quite tedious to access these databases manually, especially if you have a lot of repetitive
work to do. Biopython attempts to save you time and energy by making some on-line databases available
from Python scripts. Currently, Biopython has code to extract information from the following databases:
Entrez (and PubMed) from the NCBI See Chapter 9.
ExPASy See Chapter 10.
SCOP See the Bio.SCOP.search() function.
The code in these modules basically makes it easy to write Python code that interact with the CGI
scripts on these pages, so that you can get results in an easy to deal with format. In some cases, the results
can be tightly integrated with the Biopython parsers to make it even easier to extract information.
16

2.6

What to do next

Now that youve made it this far, you hopefully have a good understanding of the basics of Biopython and
are ready to start using it for doing useful work. The best thing to do now is finish reading this tutorial,
and then if you want start snooping around in the source code, and looking at the automatically generated
documentation.
Once you get a picture of what you want to do, and what libraries in Biopython will do it, you should
take a peak at the Cookbook (Chapter 18), which may have example code to do something similar to what
you want to do.
If you know what you want to do, but cant figure out how to do it, please feel free to post questions
to the main Biopython list (see http://biopython.org/wiki/Mailing_lists). This will not only help us
answer your question, it will also allow us to improve the documentation so it can help the next person do
what you want to do.
Enjoy the code!

17

Chapter 3

Sequence objects
Biological sequences are arguably the central object in Bioinformatics, and in this chapter well introduce
the Biopython mechanism for dealing with sequences, the Seq object. Chapter 4 will introduce the related
SeqRecord object, which combines the sequence information with any annotation, used again in Chapter 5
for Sequence Input/Output.
Sequences are essentially strings of letters like AGTACACTGGT, which seems very natural since this is the
most common way that sequences are seen in biological file formats.
There are two important differences between Seq objects and standard Python strings. First of all, they
have different methods. Although the Seq object supports many of the same methods as a plain string, its
translate() method differs by doing biological translation, and there are also additional biologically relevant
methods like reverse_complement(). Secondly, the Seq object has an important attribute, alphabet, which
is an object describing what the individual characters making up the sequence string mean, and how they
should be interpreted. For example, is AGTACACTGGT a DNA sequence, or just a protein sequence that
happens to be rich in Alanines, Glycines, Cysteines and Threonines?

3.1

Sequences and Alphabets

The alphabet object is perhaps the important thing that makes the Seq object more than just a string.
The currently available alphabets for Biopython are defined in the Bio.Alphabet module. Well use the
IUPAC alphabets (http://www.chem.qmw.ac.uk/iupac/) here to deal with some of our favorite objects:
DNA, RNA and Proteins.
Bio.Alphabet.IUPAC provides basic definitions for proteins, DNA and RNA, but additionally provides
the ability to extend and customize the basic definitions. For instance, for proteins, there is a basic IUPACProtein class, but there is an additional ExtendedIUPACProtein class providing for the additional
elements U (or Sec for selenocysteine) and O (or Pyl for pyrrolysine), plus the ambiguous symbols
B (or Asx for asparagine or aspartic acid), Z (or Glx for glutamine or glutamic acid), J (or Xle
for leucine isoleucine) and X (or Xxx for an unknown amino acid). For DNA youve got choices of IUPACUnambiguousDNA, which provides for just the basic letters, IUPACAmbiguousDNA (which provides for
ambiguity letters for every possible situation) and ExtendedIUPACDNA, which allows letters for modified
bases. Similarly, RNA can be represented by IUPACAmbiguousRNA or IUPACUnambiguousRNA.
The advantages of having an alphabet class are two fold. First, this gives an idea of the type of information
the Seq object contains. Secondly, this provides a means of constraining the information, as a means of type
checking.
Now that we know what we are dealing with, lets look at how to utilize this class to do interesting work.
You can create an ambiguous sequence with the default generic alphabet like this:
>>> from Bio.Seq import Seq

18

>>> my_seq = Seq("AGTACACTGGT")

>>> my_seq
Seq(AGTACACTGGT, Alphabet())
>>> my_seq.alphabet
Alphabet()
However, where possible you should specify the alphabet explicitly when creating your sequence objects
- in this case an unambiguous DNA alphabet object:
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet