How to get the maximum number of hits in BLAST 2.2.31+?

Question

[Neha shri]

Hi,

I have a locally created database which contains thousands of protein sequences . I want to check the positive substitutions in every sequence with reference to the target protein as random substitutions were made in every sequence. The format specifier I am using is "positive -Number of positive-scoring matches".

The command line used-

Blastp -query -db -outfmt "7 ssequid  mismatch  positive  ppos "

Query is "Whenever I am running BLAST , it generates only 500 hits, which is may be the default, How can I get the output for all the sequences.

I am new to using command line BLAST. Any help will really be appreciated.

Answer 1

[Protostome]

Use either of the following flags (taken from blastp -help)

 -max_target_seqs <Integer, >=1>
   Maximum number of aligned sequences to keep 
   Not applicable for outfmt <= 4
   Default = `500'

OR:

 -num_descriptions <Integer, >=0>

   Number of database sequences to show one-line descriptions for
   Not applicable for outfmt > 4
   Default = `500'
    * Incompatible with:  max_target_seqs
 -num_alignments <Integer, >=0>
   Number of database sequences to show alignments for
   Default = `250'

[Neha shri]

Thank you so much :) I am able to do it now.

Could you please also tell me a way to get the full fasta sequences in the output instead of only their sequence ids?