surprisingly hard: Going from Genbank Accession number to Genome Name

[berthubert]

Hi everybody,

I wrote an automated FASTQ based 16S rrna searcher, so you give it your FASTQ and it tells you which 16S matches it best. Although most people should know which genome they sequenced, I enjoy my computer telling me what I did ;-) It may also help you spot contaminants. Code on https://github.com/beaumontlab/antonie

However - the Green Genes database (at http://greengenes.secondgenome.com/downloads ) gives me a Genbank Accession Number, like this:
Best current guess: Genbank GU198115.1

But I'd like to show my user "Pseudomonas fluorescens strain LMG 7207 16S ribosomal RNA gene, partial sequence."

I have found several e-utils queries that work, like http://eutils.ncbi.nlm.nih.gov/entre...ta&retmode=xml

But these often deliver the entire genome, which I really don't need! Is there a way to send a limited query to only get TSeq_defline or TSeq_orgname?

Or alternatively, is there a database of accession numbers/names that I can download somewhere?

Thanks!

[rhinoceros]

gi2taxid

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=nucleotide&db=taxonomy&id=???

taxid2data

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=???

You'll probably first need to turn those accessions to gis..

[berthubert]

Hi,

Thanks, this works (once I've figured out the gi!). This URL appears to deliver the GI based on the accession number: http://eutils.ncbi.nlm.nih.gov/entre...somedomain.com

And it also delivers a human friendly name!

EDIT: oops, for some accession numbers (like AM181176.4) it still delivers far too much data ;-(

Thanks!

[berthubert]

Output now looks like this, but for *some* accession numbers, the URL still returns a huge amount of data ;-(

$ ./16ssearcher gg_13_5.fasta P1-1-35_S5_L001_R*fastq
-> Best current guess: 1111855 (2024) -> Genbank HQ911364.1
ORGANISM Pseudomonas fluorescens
2 potentials out of 240 candidates -> Best current guess: 1111132 (3456) -> Genbank GU437272.1
ORGANISM uncultured bacterium
10 potentials out of 2390 candidates -> Best current guess: 1105115 (3457) -> Genbank JF262574.1
ORGANISM Pseudomonas sp. UYSO19
158 potentials out of 186282 candidates -> Best current guess: 790134 (3652) -> Genbank HM190225.1
ORGANISM Pseudomonas marginalis pv. marginalis
363 potentials out of 264000 candidates -> Best current guess: 589242 (3946) -> Genbank GU198113.1
ORGANISM Pseudomonas fluorescens
364 potentials out of 264069 candidates -> Best current guess: 588382 (4362) -> Genbank GU198112.1
ORGANISM Pseudomonas fluorescens
368 potentials out of 267000 candidates -> Best current guess: 585665 (4362) -> Genbank GU198115.1
ORGANISM Pseudomonas fluorescens
2353 potentials out of 683524 candidates -> Best current guess: 16810 (4644) -> Genbank AF336349.1
ORGANISM Pseudomonas fluorescens
3049 potentials out of 999000 candidates -> Best current guess: 3860764 (4980) -> Genbank NC_012660.1
ORGANISM Pseudomonas fluorescens SBW25
3431 potentials out of 1166308 candidates -> Best current guess: 4408488 (4980) -> Genbank AM181176.4
ORGANISM Pseudomonas fluorescens SBW25


Forging on...

[berthubert]

And we have a winner, thanks to John Eargle on #bioinformatics:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=docsum&id=AE000520

Where AE000520 is the Accession Number. Thanks!