Question: Alignments As Queries In Blast
0
gravatar for eddie.im
5.7 years ago by
eddie.im130
Brazil
eddie.im130 wrote:

Hi guys, i'm reading a paper and i'm not understanding the following note:

Alignments were made using IGRs (intergenic regions) from S. meliloti as queries in BLAST comparisons against the aforementioned eight a-proteobacterial genomes.

It means that they used the aligned regions as blast queries against the 8 genomes? or they blasted the IGRs against the genomes and then aligned? I'm really confused...

Bellow follow the entire paragraph

Alignments were made using IGRs from S. meliloti as queries in BLAST comparisons against the aforementioned eight a-proteobacterial genomes. We used WU-BLAST 2.0 (23 October 2003; http://blast.wustl.edu; López et al., 2003) with a word size of eight, and default parameters otherwise. Align- ments with an E-value < 0.00001 and a length ? 50 nt were kept and used as input data for eQRNA and RNAz. An additional set of alignments was obtained using 57 known RNAs (54 tRNAs, tmRNA and the 2 copies of RmInt1 associated to ISRm2011–2) as queries. These RNA alignments were gen- erated using similar BLAST parameters, and were used to assess the sensitivity and specificity of the computational analysis.

conservation alignment blast • 1.3k views
ADD COMMENTlink modified 4.2 years ago by Biostar ♦♦ 20 • written 5.7 years ago by eddie.im130

Actually I want to ask to you that how did you accomplish that means blasting against any given intergenic regions V/S query genome

ADD REPLYlink written 2.5 years ago by deepaksen0810960
0
gravatar for Devon Ryan
5.7 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

BLAST (the "A" is for "alignment") returns local alignments of the queried sequences (IGRs) against the 8 genomes. So they blasted the IGRs and that produced alignments for each.

ADD COMMENTlink written 5.7 years ago by Devon Ryan93k

Oh of course! Now i see, i made a confusion because i was reading another paper that they used a multiple alignment aproach. Thanks!

ADD REPLYlink written 5.7 years ago by eddie.im130
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1841 users visited in the last hour