What should be the best parameter to perform blastp

Question

[Nelo]

I need to perform blastp having a local database of ~>1500 fasta sequences against a specific protein query sequences. So what should be the percent identity, coverage of blast hits, e-value, bit score for getting a good protein sequence.

Another question is out of all this parameter which one should i look in consideration first while performing blastp

By the way I am using command line for this

Answer 1

[lieven.sterck]

why not start with the default parameter settings and take it from there?

(default will do just fine in most cases, only when having unexpected results or input you can consider changing the default)

[Nelo]

I first started with dafault value but the thing is its giving me very unwanted hits

I just wanted to know other than e-value and bitscore, if we have to set another parameter other than these two, should i first consider percent identity or query coverage ? And what should be the value of them for BLASTP

[GenoMax]

We have no idea what your data is about so it would be hard to give you recommendations. There are no best parameters for most tools. You have to experiment with options that are logically applicable for your data to see what you get. While the hits may be "unwanted" they would be scientifically logical for parameters that were in use.