Tweet
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 ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria, 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:
Genome (file) 2:
etc...
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
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 ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria, 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:
Code:
>NZ_NMDP01000102.1 Escherichia coli strain MOD1-EC6062 >NZ_NMDP01000103.1 Escherichia coli strain MOD1-EC6062
Code:
>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