My good friend Deepak had a quote in his blog from Lincoln Stein about making bioinformatics as much an everyday tool to the practicing biologist as a pipettor ( a device used to dispense liquids by experimental biologists and chemists)..
I totally agree, but think we are quite far away. For example this morning I had to obtain the sequence of 772 swissprot entries ,which were part of an alignment for some downstream analysis. Of course my first choice was to query the NCBI -Entrez database. I soon realized that NCBI query box did not return any results for the first few queries I tried, all of which were probably new Uniprot/SwissProt IDs ( for eg. .sequence ids Q57T52_SALCH ,Q325Y4_SHIBS )
Disappointed , I turned to the EBI search engine. Within seconds I realized that the EBI indeed does indeed serve up all of entries. SO there are a subset of uniprot entries that the NCBI does not have in its database.
Out of sheer curiosity I entered the queries that drew a blank at the NCBI into Google.
Wonder of Wonders google pulled up all of the hard to find UniProt entries as the very first Match.
Thanks to the increasing use of publicly accessible web service APIs , Google is becoming more and more aware of a lot of very specific sequence data.
I will be very happy when I can type Q57T52_SALCH calc=MW and get an answer back from right inside google. Maybe that day bioinformatics will move one step closer to becoming just another tool.
Till then I am stuck with learning about Equery and WSDL and SOAP and so on..
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3 responses so far ↓
business|bytes|genes|molecules // June 21, 2007 at 12:55 am
[...] Yesterday, I blogged about removing barriers to bioinformatics. It would appear that we are not quite there yet. [...]
Animesh // June 21, 2007 at 6:45 am
Cool, incorporate the gapped alignment [ http://en.wikipedia.org/wiki/Dynamic_programming ] and the extreme-value-distribution [ http://en.wikipedia.org/wiki/Generalized_extreme_value_distribution ] rolled with their AI expertise [ http://norvig.com/ ] and we have something cooler
A query like http://www.google.co.in/search?hl=en&as_qdr=all&q=ccatcagcaa+http%3A%2F%2Fwww.ncbi.nlm.nih.gov&btnG=Search&meta= should bring all the sequence close to pattern “ccatcagcaa”!
Back on the NCBI horse « The Omics world // July 13, 2007 at 8:50 pm
[...] 13th, 2007 · No Comments I have been working a lot with alignments in Jalview and had blogged about how Google can find Uniprot IDs better than NCBI ..well it turns out that NCBI did indeed have most of the Uniprot sequences I was looking [...]