tag:blogger.com,1999:blog-10781944.post7750354947740637767..comments2024-03-28T00:36:36.460-07:00Comments on The Tree of Life: NCBI. Why? Why? Why is the default database for blasting "human G+T"Jonathan Eisenhttp://www.blogger.com/profile/07953790938128734305noreply@blogger.comBlogger8125tag:blogger.com,1999:blog-10781944.post-56662590644007524852012-08-31T07:22:54.309-07:002012-08-31T07:22:54.309-07:00Absolutely agree. Another pet peeve: default on f...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.<br />Anonymoushttps://www.blogger.com/profile/06782916293904835983noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-5688082664627055842012-08-30T18:02:17.416-07:002012-08-30T18:02:17.416-07:00Talking about nr, I found recently a "funny&q...Talking about nr, I found recently a "funny" information <a href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml" rel="nofollow"> there </a>:<br />"""<br />Nucleotide Sequence Databases<br />nr<br />All GenBank + RefSeq Nucleotides + EMBL + DDBJ + PDB sequences (excluding HTGS0,1,2, EST, GSS, STS, PAT, WGS). No longer "non-redundant".<br />"""<br />OK, NCBI: could you change this misleading name please? Something like "anr" (almost non-redundant")...Anonymoushttps://www.blogger.com/profile/12524553542055635920noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-4404082561230464442012-08-30T17:24:38.958-07:002012-08-30T17:24:38.958-07:00I wonder how much that default reduces their serve...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.Marmadukehttps://www.blogger.com/profile/08821077486103359942noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-27485837024324269072012-08-30T16:21:35.697-07:002012-08-30T16:21:35.697-07:00Just another reason to switch to hmmer3!Just another reason to switch to hmmer3!Anonymoushttps://www.blogger.com/profile/09625040758735497849noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-59329797822071678792012-08-30T14:45:55.932-07:002012-08-30T14:45:55.932-07:00Having the default db be human is annoying, but if...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.<br /><br />Alternatively, you might bookmark the microbial genome blast page: <br /><br />http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?PAGE=MegaBlast&PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&BLAST_SPEC=MicrobialGenomes<br /><br />Sandra Porterhttps://www.blogger.com/profile/09209950581908760880noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-56865398609272643042012-08-30T14:19:38.793-07:002012-08-30T14:19:38.793-07:00They changed this awhile ago. I often use this que...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.tintmylfhttps://www.blogger.com/profile/00485484659873848444noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-85371192949740669182012-08-30T14:01:56.595-07:002012-08-30T14:01:56.595-07:00Well, maybe now we will get one ...Well, maybe now we will get one ...Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-43990353673136172742012-08-30T14:00:13.655-07:002012-08-30T14:00:13.655-07:00I wrote NCBI about this when they changed it a few...I wrote NCBI about this when they changed it a few years ago... didn't get a response.arturgreenswardhttps://www.blogger.com/profile/04066563835707554590noreply@blogger.com