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 (60%), 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 97Query: 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
normal i have 60% of identities and 5 gaps, when i put -m8 option i have 63.55% identities and 4 gaps..
any reason??
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