Tag: FASTA

BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024

Easily generate BLAST FASTA files yourself!

In April 2024, the FASTA (sequence text) files of the sequences in the Basic Alignment Search Tool (BLAST) databases will no longer be available on the FTP site. However, you can easily generate FASTA files yourself from the formatted BLAST databases by using the BLAST utility blastdbcmd that comes with the standalone BLAST programs. This provides you the flexibility to generate organism-specific FASTA files using NCBI’s taxonomy IDs for specific organisms or groups.

See the examples below and the BLAST Command Line Applications User Manual for more details on the standalone BLAST programs and working with the BLAST databases. Continue reading “BLAST FASTA Files Will No Longer Be Available on the FTP Site Effective April 2024” →

New wizard for submitting mRNA sequences to GenBank

Do you submit eukaryotic nuclear mRNA sequences to GenBank? A new mRNA submission wizard is available! Built on the modern Submission Portal framework, this new wizard will bring you an enhanced experience, including:

- Guided submission experience specific for mRNA sequences
- Automated trimming of vector and removal of short sequences
- Easier input for source metadata
- New feature annotation web forms for coding region (CDS) and untranslated region (5’ UTR, 3’ UTR)
- Extensive feature previews (Figure 1)
- Faster sequence processing and accession assignment
- Access to a fix error workflow prior to accession assignment

Watch a short video (4 min) to see how to annotate CDS features in this new wizard! Continue reading “New wizard for submitting mRNA sequences to GenBank” →

Introducing the new Virus Sequence Search Interface

BLAST is a powerful search tool, but often a search is just the beginning of the journey. We put ourselves in the shoes of a researcher who has just sequenced a handful of samples from the latest viral outbreak and tried to understand what information would be most useful. We also reached out to researchers in the field and asked: a) what questions do they really want to answer? and b) how can NCBI best provide the answers? Based on insights from those questions and answers, we developed the new Virus Sequence Search Interface (Fig. 1). The Search Interface is an NCBI Labs project, which means it is an experimental project, and we may modify the resource based on your feedback and experiences.

Figure 1. The Virus Sequence Selection Interface. — **Figure 1.** The Virus Sequence Selection Interface. The Virus Sequence Selection Interface accepts as input nucleotide and protein accessions, as well as FASTA and plain-text formatted sequences. The user selects either “Nucleotide” or “Protein,” depending on the sequence type, and selects the virus type from the pull-down menu below the text entry field.

Continue reading “Introducing the new Virus Sequence Search Interface” →

New Influenza Virus Submission Wizard Makes Flu Sequence Submissions Easier

NCBI now offers a flu sequence submission wizard that makes submissions easier and will provide you with accession numbers sooner. To get started, sign in to NCBI, go to the Submission Portal and choose the link for “Ribosomal RNA (rRNA), rRNA-ITS or Influenza sequences” from the GenBank section.

Continue reading “New Influenza Virus Submission Wizard Makes Flu Sequence Submissions Easier” →

Designing exon-specific primers for the human genome

A common task facing geneticists is to assay for sequence changes at particular locations in genes. These assays are often looking for changes in the coding exon of genes, and the target sequences are typically amplified using PCR from genomic DNA using a pair of specific primers. In this article, we will show you how to use NCBI Reference Sequences and Primer-BLAST, NCBI’s primer designer and specificity checker, to design a pair of primers that will amplify a single exon (exon 15) of the human breast cancer 1 (BRCA1) gene.

Here are the steps to follow to design primers to amplify exon 15 from human BRCA1:

Continue reading “Designing exon-specific primers for the human genome” →

How To Format Sequence Data For GenBank Submissions

Submitting sequences to GenBank can seem complicated at first, but starting with a solid foundation in the form of a properly formatted file will make the process go smoothly.

Before submitting sequence data to GenBank, the data must be formatted correctly, the most common file format being FASTA. This post will show you how to create a FASTA file for submitting single- and multiple-nucleotide sequences.

Submitters can upload FASTA-formatted sequence files using NCBI’s stand-alone software Sequin, command line tbl2asn or our web-based submission tool BankIt.

The image below depicts a single sequence in FASTA format. For multiple sequences, such as those of population or phylogenetic studies, environmental samples, and batch sequences of the same gene, create the file using the steps below and put the set of sequences together in a single FASTA file.

Here is how to create the FASTA file:

Continue reading “How To Format Sequence Data For GenBank Submissions” →