Count hits in Local Blast (Blast+)

[Hel]

Hi there,

I have just run a standard Local Blast using Blast+:
blastx -db mydb -query mysample -evalue 0.00001 -out blastxresult

and I wonder: How to check the number of blast hits? The number of 'significant' cites in the output file is the number of hits?


I alternative tried other approaches such as get a tabular or a xml format:
blastx -db mydb -query mysample -evalue 0.00001 -outfmt 6 -out tab_blastxresult
The number of rows is the number of hits?

blastx -db mydb -query mysample -evalue 0.00001 -outfmt 5 -max_target_seqs 10 -out xml_blastxresult
No idea about count hits in this format.


Any help will be appreciated,

[GenoMax]

Number of rows that refer to your query sequence will be the "significant" (this definition depends on options you select for blast e.g. e value cutoff) hits for that query in tabular format. Are you just interested in the count (and not the actual hits)?

[maubp]

Note that you can get multiple rows from the same match in the tabular output if multiple HSPs are given (e.g. if the target sequence contains a repeat, you could get two pairwise alignments which give HSPs passing the e-value threshold).

You might want to look at parsing the BLAST output using BioPerl, Biopython, etc if you need to do anything more complicated with your analysis.