BLAST step of GO enrichment analyses

Question

[Ginsea Chen]

Dear all!

I used nr database which download from NCBI as query database in BLAST step of GO analyses, and then I loaded this result file into Blast2go basic software. However, lots of sequences had no hits. I don't know what happened and whether this bad blast will influence my GO results or not?

Answer 1

[Istvan Albert]

There are different strategies that blast can be run with that will differ in sensitivity and speed: megablast, discontiguos, megablast, blastn, blastn-short etc in addition you can also set different alignment parameters.

Depending on the situation you may want to run blast with more sensitive strategies.