I have often blogged about my trials and tribulations with the NCBI database.This morning I was trying to locate all the kappa light chain genes from the NCBI database.
I tried the following search
Immunoglobulin kappa mouse in the Genome database subsection.
The results I got were a curious mix of microbe genomes ranging from Aspergillus Niger to Salmonella enterica. Maybe I left my search skills at home or my eyes are playing tricks on me.
Addendum: Eric Jane from Uniprot showed me how to do the same query on Uniprot beta. Uniprot really rocks. Not only could I do the query , but also downloaded the results in batch mode as fasta sequences and in the xml format.Thanks eric , I would definitely recommend uniprot beta to everyone. Isabelle phan from uniprot did post an excellent screencast detailing the features of uniprot beta at this link on Bioscreencast.com . Do check it out as well as Erics comments below.
6 responses so far ↓
Eric Jain // September 13, 2007 at 8:08 pm
If you run the same query on UniProt you’ll get slightly more useful results, I hope: http://beta.uniprot.org/uniprot/?query=Immunoglobulin+kappa+mouse&sort=score
Unfortunately the search engine doesn’t know (yet) that “Ig” is a synonym for “immunoglobulin”, and “mouse” should either be restricted to the “organism” field (click on the suggestion) or, better, replaced with its TaxID (use the query builder):
http://beta.uniprot.org/uniprot/?query=(%22immunoglobulin+kappa%22+OR+%22ig+kappa%22)+AND+organism:10090
If you need to go back to NCBI you can then map these results to GenBank or RefSeq or GeneIDs:
http://beta.uniprot.org/jobs/NZIR
Eric Jain // September 13, 2007 at 8:12 pm
Looks like the second link got truncated, so let’s try this:
http://tinyurl.com/2dlhjm
The query actual query is:
(”immunoglobulin kappa” OR “ig kappa”
AND organism:10090
Hari Jayaram // September 13, 2007 at 9:23 pm
I tried a similar query as the one you suggested as an all database query on NCBI , but sadly NCBI returns NONE
Also the tinyURL for the query with the faulty NCBI search results is
http://tinyurl.com/2cfbe8
I will try the query on Uniprot Beta as you suggested.
thanks Eric
harijay // September 13, 2007 at 9:37 pm
Wow beta.uniprot.org search works so much better- Thanks a tonne
Just curious..does uniprot have something like “blink”?
Hari
Eric Jain // September 14, 2007 at 8:28 am
Not exactly, but you can use UniRef to get sequences with 50%, 90% or 100% identity to another sequence, e.g. here are the three clusters for P00750:
http://beta.uniprot.org/uniref/?query=member%3AP00750
You can also use sequence checksums or map identifiers from other databases if you don’t have a UniProt accession to start with…
Why are our bioinformatics workflows so complicated! « The Omics world // September 17, 2007 at 3:59 pm
[...] # Use EBI to get the same sequence data ( Value 10 : Ease 8 ) [...]
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