I'm almost confused on blastx output length result. So the questions are:
Query= NODE_2160645-0;57 Length=82
ref|XP_002833304.1| PREDICTED: hypothetical protein LOC100444373 [Pongo abelii]
Length=134
Score = 37.7 bits (86), Expect = 0.74
Identities = 11/14 (78%), Positives = 14/14 (100%), Gaps = 0/14 (0%)
1)Query length has been reported 82! (but It's 57) ?!
2)The Identities number reported in Protein digit (the number of identities protein =11 so if want the number of base 11*3=33 bp) so the length of hit (134) is in bp or protein pare !? if it's in bp why it's not dividable by 3 ?! (the result 134/3 is not integer)
Thanks
Question 1 Solved [It's human mistake]
NODE_2160645-0;57 GTAAGGTGAGAAAAAAAAAAAACGGAAGACTTGCCTTTCTCCAGTCCATTCCGTTCAATC CATTCCATTCCAGTCCATTCCA
blastx -query contigs.out -db nr .....
version: 2.2.24+
Query= NODE_2160645-0;57
Length=82
Sequences producing significant alignments: Score(Bits) EValue
ref|XP_002833304.1| PREDICTED: hypothetical protein LOC100444373... 37.7 0.74
ref|XP_002833304.1| PREDICTED: hypothetical protein LOC100444373 [Pongo abelii]
Length=134
Score = 37.7 bits (86), Expect = 0.74
Identities = 11/14 (78%), Positives = 14/14 (100%), Gaps = 0/14 (0%)
Frame = -1
Query 82 WNGLEWNGLNGMDW 41
WNG++WNG+NGMDW
Sbjct 100 WNGIQWNGMNGMDW 113
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Effective search space used: 152859517525
•
written
by
khikho
Subject length (134) is given in amino acids, not nucleotide, because it is an amino acid database. The length of the alignment is 14 out of 134 aa.
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Please help by posting the query sequence fasta entry (only NODE_2160645 !), blastx version and commandline parameters and the full alignment output for this hsp. That will give a reproducible example.
Because of formatting I put them in Answer part