how to choose the blastp output results?

Question

[1901919946]

I hava a non-redundant gene catalog(metagenomics) and alignment to the ARDB database. The output results is M8 format which just like:

============================================================================================

ASD044-F3_gene_209671   SBV91433.1      25.9    27491   14520   913     749     24386   526     26013   0.0e+00 5526.4
ASD044-F3_gene_209671   SBV91433.1      20.9    30325   17828   1139    1005    28256   3739    30971   0.0e+00 1155.6
ASD044-F3_gene_209671   SCH57567.1      26.6    14223   7932    471     15991   29028   44      12950   0.0e+00 3371.6
ASD044-F3_gene_209671   SCI89204.1      26.6    14223   7932    471     15991   29028   44      12950   0.0e+00 3371.6
ASD044-F3_gene_209671   OKZ61661.1      21.9    6119    3475    192     1925    7461    71      5467    3.0e-149        543.5

..........................................

A query alignment to more than two results,so how do i chose the result? Maybe evalue or bitscore?

Thanks!

[lieven.sterck]

what kind of blast did you ran? it does not look like a blastp output.

Depends what you want to achieve or what the specific reason is for selecting a single hit.

[1901919946]

I use diamond to do it ： diamond blastp -d ardb -q mySample.faa -e 0.00001 -o ardb.m8

Answer 1

[karthic]

While running the blast, I generally specify the evalue cutoff required in the query itself and when there are too many hits for the same sequence, i include query coverage. This way I can filter out my blast results those having low query coverage value.

Thanks

KK