Go Back   SEQanswers > Applications Forums > Metagenomics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Doing local blast. No alias or index file found for nucleotide database? hyates Bioinformatics 2 03-09-2015 04:22 AM
How can I write a bash command to blast local nt database? hyates Bioinformatics 5 03-05-2015 09:30 AM
Creating local blast+ database for mouse build 37 npatel Bioinformatics 7 03-04-2013 08:02 AM
BLAST database error - when changing to new BLAST+ local program biobio Bioinformatics 4 06-15-2011 05:20 AM
Create local BLAST database SeqClark Bioinformatics 2 03-07-2011 01:17 AM

Thread Tools
Old 01-09-2018, 12:39 AM   #1
Junior Member
Location: Oslo

Join Date: Jan 2018
Posts: 1
Question Generate local blast database with RefSeq bacteria AND taxonomy

Dear all,

I would like to be able to create my own custom local blast database, as this may be relevant in many different situations in bioinformatics. In this case, I hope to make a database containing all the latest versions of the bacterial genomes found in RefSeq. For starters, I have downloaded bacterial genomes (assemblies) from, using information in the "assembly_summary.txt" to fetch the latest genome versions only. As a result, I now have almost 104,000 files (one per bacterial genome) containing one or multiple contigs. So far, so good.

Each contig within a genome has a header containing the NCBI accession number ++, i.e.:

Genome (file) 1:

>NZ_NMDP01000102.1 Escherichia coli strain MOD1-EC6062

>NZ_NMDP01000103.1 Escherichia coli strain MOD1-EC6062
Genome (file) 2:

>NZ_NOBY01000102.1 Escherichia coli strain MOD1-EC5816

>NZ_NOBY01000115.1 Escherichia coli strain MOD1-EC5816

I now want to associate all genomes with a taxonomy (taxid?), as I understand this is important in many applications. For example, by blasting to my local database, I want to be able to quickly determine from which bacterium my blast query sequence originates.

My questions are therefore:

1. How do I find the taxon ID for all the bacterial genomes in question?

(Note: These are genomes from ../genomes/refseq/bacteria, not ..refseq/release/bacteria)?

2. How do I incorporate that information into my genome files and/or final local database?

I suspect I first have to link up the NCBI accession number in the headers to a taxon ID in some way, but I'm not sure how to do that, or in what format it should be.

All answers are highly appreciated!

Kind regards,

Even Sannes Riiser,

PhD candidate, University of Oslo, Norway
evensrii is offline   Reply With Quote

blast, local, refseq, taxid, taxonomy

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 08:40 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO