NOTE: This version is Saccharis 1.0 and is now debracated -- the new version Saccharis 2.0 can be found Here

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SACCHARIS

Sequence Analysis and Clustering of CarboHydrate Active enzymes for Rapid Informed prediction of Specificity (SACCHARIS), is a PERL based pipeline designed to improve functional predictions of uncharacterized sequences for any CAZyme or CBM family currently maintained on the CAZy website or within user-defined datasets.

Citation

When using SACCHARIS please site the following paper:

Jones DR, Thomas DK, Alger N, Ghavidel A, Inglis GD, Abbott DW. SACCHARIS: An automated pipeline to inform discover of new carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets. Biotechnology for Biofuels, 11 (2018), p. 27, DOI: 10.1186/s13068-018-1027-x.

License

This software is distributed under the terms of the GPL, version 2 or later, excepting that:

• The third party programs and scripts used by SACCHARIS are covered by the terms of their respective licenses

Additional Scripts

With this package I have included a copy of:

• fasta_rmSmall.pl
  • This script screens a fasta file and will remove sequence data where length of sequence is smaller than a user definined minimum length

Requirements

• Perl Libraries
  • Bio::Seq, Bio::SeqIO
  • Date::Calc
  • File::chdir
  • GetOpt::Long
  • HTML::TagParser (see note below)
  • List::Util
  • LWP::Simple
  • Threads
• Third Party Software
  • dbCAN
  • HMMER 3.1
  • MUSCLE
  • ProtTest 3
  • RAxML
  • FastTree (Requires version 2.1.10 or greater)
  • Fasta_subsample.pl
• Notices
  • If you experience an error pertaining to an uninitialized $esearch value, confirm you have the following packages installed
    • libwww-perl (linux)
    • LWP::Protocol::https (OSX)

Installation

1. Install all Requirements
2. Clone Repository git clone
3. Copy Scripts to a location in the PATH

HMMER Installation

1. Download HMMER
2. Extract archive
3. Copy or Move folder to /usr/local/hmmer
4. Add binaries directory to your Path

dbCAN Installation

1. mkdir /usr/local/dbcan
2. Download dbCAN
   • dbCAN-fam-HMMs.txt
   • hmmscan-parser.sh
3. Format HMM db
   • hmmpress dbcan-fam-HMMs.txt

ProtTest Installation

1. Clone Repository git clone
2. Move directory to /usr/local/prottest3

MUSCLE Installation

1. Download MUSCLE
2. Copy muscle binary to location in the path like /usr/local/bin

FastTree Installation

1. Install as per directions Here

RAxML Installation

1. Clone Repository git clone
2. Follow Directions in README to create Executables
3. Move executables to a location in the Path

Fasta_subsample.pl Installation

1. Script is included with SACCHARIS
2. Script was written by Timothy L. Bailey and William Noble
3. Script is part of the MEME Suite

Modifications - HTML::TagParser

• Tagparser.pm throws an error on line 236 - Fix - Alter Line to
  • bless $self, ref($package) || $package;

NCBI Registration - cazy_extract.pl

• NCBI E-Utilities Registration is Required for running of the cazy_extract.pl script
  • Steps Involved
    • Send email to [email protected] that includes the desired values for email address and tool name
      • eg. tool = SaccharisTool, email = your.name@domain
    • Create and account on NCBI (https://www.ncbi.nlm.nih.gov/account/) in the Settings page create and API Key
    • Uncomment and Modify Lines 31-33 of cazy_extract.pl - use the information from steps 1 and 2 to modify the script
• cazy_extract.pl will not run without this information

Modify User Data Headers

• Run the following in a terminal window with <insert_here> replaced with your base file name
  • perl -pe 's/\>/$& . U . sprintf("%08d", ++$n) . " "/ge' <insert_here>.fasta > <insert_here>_mod.fasta

Running SACCHARIS

• In terminal follow Usage as given by
  • Saccharis.pl ; or
  • Saccharis.pl -m