Question: Concatenating default BLAST ouputs
0
gravatar for Ric
4 months ago by
Ric290
Australia
Ric290 wrote:

Hi, I split my FASTA file into many chunks and ran BLAST with default settings against a database. Is there a way to concatenate default BLAST outputs?

TBLASTN 2.3.0+


Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.



Database: NbV1ChF
           19 sequences; 2,742,960,125 total letters



Query= mRNA_2_cds mRNA_2
gene_2|id=AT4G34310.1:evalue=0.0:annot='alpha/beta-Hydrolases
superfamily protein';id=Solyc04g079280.2.1:evalue=0.0:annot='LipA
and NB-ARC domain protein'

Length=1196
                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

NbV1Ch10                                                              659     0.0  
NbV1Ch13                                                              657     0.0

Thank you in advance,

Michal

blast alignment • 192 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by Ric290
1

What is the use case for concatenating the results? These chunks can be parsed independently and the end results concatenated.

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax76k

Do you need to use that output format? It might make more sense to concatenate a blast tabular output for instance.

ADD REPLYlink written 4 months ago by Joe15k

I tried to use bp_search2gff.pl (part of BioPerl) which only supports the pairwise BLAST output. The goal is to speed up tBLASTn.

ADD REPLYlink written 4 months ago by Ric290

I guess you can concatenate them in multiple ways. Even with copy/paste. But one important thing to consider is that BLAST won't find an alignment but subsequences inside your sequence with high score as alignment. So it can return a much shorter sequence. And it could even be that this shorter sequence is not even the best alignment despite having a high partial score.

ADD REPLYlink written 4 months ago by juanjo75es70
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