BioPythonUtils

BioPython Utilities for Sublime Text 3.

Install

Install BioPythonUtils using Package Control. If you don't have Package Control see https://sublime.wbond.net.

The BioPython 1.68 code is bundled with this package, you do not need to install it.

Configure

Add your email address and BLAST defaults to your Settings file.

{
    "email_for_eutils": "[email protected]",
    "entrez_retmax": 1000,
    "remote_blast_app": "blastp",
    "remote_blast_db": "nr",
    "remote_blast_format": "Text"
}

The email address is required if you want to download from NCBI using EUtils.

Commands

First select the relevant text, then run a command in the Tools -> BioPythonUtils menu.

• "Translate"
• "Get Sequences by Search"
• "Get Sequences by Id"
• "Get Sequences by Taxon"
• "Remote BLAST"
• "Genbank To Fasta"

"Translate"

Translates the selected text, which can be 1 or more entries in Fasta format or 1 or more entries of plain text. For example:

>2
atgctatcaatcgcgattctgcttctgctaatagcagagggctcctctcaaaattacaca
ggaaatcctgtgatatgcctggggcaccatgctgtgtccaatgggacaatggtgaaaacc
>1
atgctatcaatcacgattctgttcctgctcatagcagagggctcctctcagaattacaca
gggaatcctgtgatatgcctgggacatcatgctgtatccaatgggacaatggtgaaaacc

or:

atgctatcaatcacgattctgttcctgctcatagcagagggctcctctcagaattacaca
gggaatcctgtgatatgcctgggacatcatgctgtatccaatgggacaatggtgaaaacc

atgctgtcaatcacgattctgttggtgctcatagcagagggctcctctcagaattacacg
gggagtcctgtgatatgcctgggacatcatgctgtatccaatgggacaatggtgaaaacg

Translation starts at the first codon and continues to the last, regardless of stop codons.

"Get Sequences by Search"

Queries NCBI Nucleotide using Entrez search service and the selected text and downloads the sequence results in GenBank format. For example:

human[ORGN] AND AKT1[GENE]

The default maximum number of records downloaded is 20, if you want more than 20 set the value in your "Settings - User" file ("entrez_retmax").

"Get Sequences by Id"

Downloads sequence from NCBI using the selected ids. Ids can be delimited by commas, returns, or space. For example:

KC781785 2

or:

2
KC781786

or:

284218, 203807

"Get Sequences by Taxon"

Downloads a taxon as GenBank format entries from NCBI using the selected NCBI Taxonomy ids. Ids can be delimited by commas, returns, or space.

"Remote BLAST"

Sends the selected Fasta format or "plain" sequence(s) to the BLAST server at NCBI and retrieves the results. You can set the application, database, and result format using the Command Palette. You can also set some default values in your "Settings - User" file ("remote_blast_app", "remote_blast_format"). Note that the available databases change depending on the BLAST application.

"Genbank To Fasta"

Creates Fasta format records from the selection, 1 or more GenBank format records.

Issues

The interaction between the plugin and various services at NCBI are synchronized, so Sublime Text is unusable while the queries ("Get Sequences*", "Remote BLAST") are running.