How to get score and identity of the whole created database in BLAST?

Question

[vinicius]

I've made a database for blast containing 615 organisms.

I've blast a nucleotide sequence against this database and it returned 242 sequences. (of 242 organisms)

Is there a way to make blast return 615 sequences?

Thanks

Answer 1

[Jean-Karim Heriche]

Increase the e-value threshold. You may also need to look at -num_alignments or -max_target_seqs (depending on your choice of -outfmt)

[vinicius]

The 242 organisms return was gotten with the increased e-value threshold. But now, I tried to set -max_target_seqs 615, with -outmft 7. But yet i'm getting a lower number of hits. It was 314 this time.

Do you have any idea?

[Jean-Karim Heriche]

You may need to combine the two options -num_alignments and -max_target_seqs. Also if the sequences are not homologous, the search may not find all the sequences with the parameters you've selected (e.g. word size, gaps).