Question about blastx output

Question

[yinbinqiu]

hi, all, I used diamond blastx to compare my transcript to the uniprot database, the command is as follows

diamond blastx -d uniprotdb.dmnd -q xxx.fa -e 1e-5 -f 6 -b 10 -o ./xxx.outfmt6 --max-target-seqs 1

The output has 12 columns, which are query id, subject id,% identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue

I see a lot of gap opens that are not 0, but I do n’t see ‘N’ in my sequence. What ’s the reason? What does the gap opens column mean?

[yinbinqiu]

got it, thank you very much.

Answer 1

[Fatima]

Gap opens: Number of gap openings Which means number of times a gap started in an alignment, so X----X is one gap opening and X-X is also one gap opening. No matter how long the gap extends gap open only counts the number of times a gap opens. You can check your alignment and count the number of times a - is appeared after a character.

N in sequence means the nucleotide is not determinable (something like NaN or NA ) due to low quality/error and it can be A/C/G/T.

Blast - Formatting Output