I really need to know why when I do a blast with the option -m8, I have different results (different % identities, and gaps). example..
normal
>tr|Q3T560|Q3T560_9GAMM Arsenite transporter ATPase-like protein OS=Acidithiobacillus caldus
GN=arsA1 PE=4 SV=1
Length = 612
Score = 612 bits (1577), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 329/546 (<strong>60%</strong>), Positives = 400/546 (73%), Gaps = 5/546 (0%)
Query: 372511 RVLLVSTDPASNVGQVFGTDIGNHITQIGQVSGLEALEIDPEAAAEDYRERIIGPIRSTL 372570
++LLVSTDPASNVGQVF +IGN IT I V+GL ALEIDP+ AA+ YRERI+GP+R L
Sbjct: 38 KILLVSTDPASNVGQVFSQEIGNKITTISTVAGLSALEIDPQQAAQQYRERIVGPVRGAL 97
Query: 372571 PEKALNSIKEQLSGACTTEIAAFDEFTALLTDPELIERYDHIVFDTAPTGHTIRLLKLPG 372630
with -m8 option
# BLASTP 2.2.25 [Feb-01-2011]
# Query:
# Database: /home/biolinux/Desktop/fasta/ars/arsenic_db_3.fasta
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
1_0 tr|Q3T560|Q3T560_9GAMM 63.55 546 194 4 372511 373052 38 582 0.0 612
In "normal" I have 60% of identities and 5 gaps, but when I put -m8 option I have 63.55% identities and 4 gaps..
Any reason?
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sebastian.f.ing •
I couldn't find legacy blast 2.2.26 release notes but this is from 2.2.26+:
ChangeLog:
-----------------------------
* 2.2.26 release.
..
Bug fixes:
..
* The percent identity calculation was wrong if the best-hit algorithm was used.
So, the most likely reason is that 2.2.25 had a bug related to -m8 output and percent identity.
Perfect way to spell out: please use the most recent version to report bugs.
how i can know what version i am using?
biolinux@biolinux-PC[biolinux] blastp -version [ 2:45PM]
blastp: 2.2.28+
Package: blast 2.2.28, build May 2 2013 18:07:25
biolinux@biolinux-PC[biolinux]
I don't know why, on the header of my blast appears BLASTP 2.2.25 [Feb-01-2011]
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sebastian.f.ing •
blastall -p blastp -d database.fasta -i sequence.fasta -m8 >out
This command invokes legacy blast, but you also seem to have blast+ installed ...
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Istvan Albert
I put
blastp -db database.fasta -query query.fasta -out out.fasta
and appears this...
Warning: (1431.1) CFastaReader: Ignoring invalid residue 8 at line 112004, position 4
Warning: (1431.1) CFastaReader: Ignoring invalid residue 6 at line 112004, position 5
Warning: (1431.1) CFastaReader: Ignoring invalid residue 1 at line 112004, position 6
Warning: (1431.1) CFastaReader: Ignoring invalid residue 4 at line 112005, position 0
Warning: (1431.1) CFastaReader: Ignoring invalid residue 2 at line 112005, position 1
Warning: (1431.1) CFastaReader: Ignoring invalid residue 4 at line 112005, position 2
Warning: (1431.1) CFastaReader: Ignoring invalid residue 6 at line 112005, position 3
Warning: (1431.1) CFastaReader: Ignoring invalid residue 9 at line 112005, position 4
Warning: (1431.1) CFastaReader: Ignoring invalid residue 2 at line 112005, position 5
and keep going.....
that it's normal?
aps, and I am using a gbk query, I mean.. query.gbk, that care?
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sebastian.f.ing •
Is it really necessary to be a FASTA file?, or can be other like a GBK file?
I apply the formatdb command...
or it's the makeformatdb command?
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sebastian.f.ing •
You may want to double check the documentation:
http://www.ncbi.nlm.nih.gov/guide/howto/run-blast-local/
Use the BLAST+ makeblastdb program (or formatdb in the legacy BLAST package) to convert a FASTA-formatted local file into a BLAST database.
It seems that you're trying to blast one fasta file against another. Note that is deprecated, you want to use makeblastdb. If that doesn't work, check that the sequence entries in your query file do not contain any invalid characters.
although one does the database, the blast is always performed against fasta file database.
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