Question: Concatenating default BLAST ouputs
gravatar for Ric
14 days ago by
Ric280 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
superfamily protein';id=Solyc04g079280.2.1:evalue=0.0:annot='LipA
and NB-ARC domain protein'

                                                                      Score     E
Sequences producing significant alignments:                          (Bits)  Value

NbV1Ch10                                                              659     0.0  
NbV1Ch13                                                              657     0.0

Thank you in advance,


blast alignment • 127 views
ADD COMMENTlink modified 11 days ago • written 14 days ago by Ric280

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

ADD REPLYlink modified 14 days ago • written 14 days ago by genomax71k

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

ADD REPLYlink written 14 days ago by Joe14k

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

ADD REPLYlink written 11 days ago by Ric280

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 13 days ago by juanjo75es60
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