How to get blastx top hit (e-score)

Question

[Biogeek]

Hi,

I need to get the blastX top hit match for each of my transcripts. How do I go about this? The output is as follows:

# Fields: Query Subject identity    aln-len mismatch    gap-openings    q.start q.end   s.start s.end   log(e-value)    bit-score
BE1 TR|A0A059LRH0|9CHLO 81.2    69  13  0   335 129 103 171 -23.4   112.8
BE1 TR|C1MRA3|MICPC 80.3    71  14  0   350 138 67  137 -23.1   111.7
BE1 TR|A0A0D2MQP4|9CHLO 76.0    75  18  0   353 129 57  131 -22.7   110.5
BE1 TR|A4S062|OSTLU 74.3    74  19  0   359 138 79  152 -22.6   110.2
BE1 TR|A0A022R8S2|ERYGU 81.2    69  13  0   335 129 92  160 -22.5   109.8

Thanks.Is there a way I can also get the gene name? I'm just getting letters as above.

Answer 1

[DG]

Depending on what programming language you use, my suggestion would be to use one of the Bio* type packages available for many of them. BioPerl for perl, BioPython for Python. Not sure what the status of BioJava is these days if that is your language of choice. There are probably also alternative packages available but those BioPerl and BioPython projects have been around forever and excel at common tasks like this. They will handle parsing BLAST output and putting it into an appropriate data structure.

BioPython Tutorial/Cookbook for BLAST

BioPerl SearchIO module