It is the little things. The little things that can sometimes eat at you. And here is one of my little pet peeves. At some point - not sure how recently - NCBI changed the default database for Blastn searching to the "human G+T" database. This Db contains human genomic and transcriptomic data.
Thursday, August 30, 2012
NCBI. Why? Why? Why is the default database for blasting "human G+T"
Subscribe to: Post Comments (Atom)
Most recent post
Another day to think, to pause, to ponder.
Panorama of Sycamore Park and the memorial to Karim A bit over 10 years ago I wrote a blog post that I repost all the time. Entitled "...
I have a new friend in Google Scholar Updates I have written about the Updates system before and if you want more information please see...
New article out from the Eisen Lab: Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarumSee Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum Paper based on PhD thesis work of Katie Dahlha...
Just got this press release by email. I am sick of receiving dozens of unsolicited press releases, especially those in topics not related ...
I wrote NCBI about this when they changed it a few years ago... didn't get a response.ReplyDelete
Well, maybe now we will get one ...ReplyDelete
They changed this awhile ago. I often use this questionable choice to my advantage when assigning homework or test questions to students by giving them a mystery sequence and seeing how many think/remember to check the specific database being searched when they do a blast search.ReplyDelete
Having the default db be human is annoying, but if you log in and change the database selection, NCBI will remember your change and the next time the default db will be the one you chose.ReplyDelete
Alternatively, you might bookmark the microbial genome blast page:
Just another reason to switch to hmmer3!ReplyDelete
I wonder how much that default reduces their server load. As tintmylf says, most people don't think about the default. If all those are just blasting against human, its probably a lot less intensive than mindlessly searching nr.ReplyDelete
Talking about nr, I found recently a "funny" information there :ReplyDelete
Nucleotide Sequence Databases
All GenBank + RefSeq Nucleotides + EMBL + DDBJ + PDB sequences (excluding HTGS0,1,2, EST, GSS, STS, PAT, WGS). No longer "non-redundant".
OK, NCBI: could you change this misleading name please? Something like "anr" (almost non-redundant")...
Absolutely agree. Another pet peeve: default on for the "mask low complexity region" flag. I don't want my searches masked unless I ask for it. If they want to return BOTH the masked and unmasked versions, fine, but when a search fails JUST BECAUSE the sequence was masked, it is REALLY ANNOYING.ReplyDelete