Alignments As Queries In Blast

Question

[eddie.im]

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.

[deepaksen081096]

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

Answer 1

[Devon Ryan]

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.

[eddie.im]

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