How to Delete Hits from an original sequence

Question

[daniellaplummer]

Hello,

Using standalone Blast, I used BlastP to align the human proteome against a bacterial proteome, this gave me a number of hits where the human proteome has been found within the bacterial proteome, I need to delete these hits from the original bacterial proteome, in order to gain non-homologous genes, I was wondering if anyone knew a method that would automatically purge the original sequence of the hits instead of doing it manually. The other option is getting blastp to show the non-hits, however I cannot work out the command for this.

Many thanks
Daniella

[Reeja]

how can i filter for significant hits? and how can i collect the ids of query sequences with a significant hits? can you share grep command for it?

Answer 1

[pld]

The easiest would be to filter for significant hits and then collect the IDs of query sequences with a significant hit. After you have this list of IDs you could write a simple script to handle this or find one of the many tools online (e.g. http://qiime.org/scripts/filter_fasta.html).

[Reeja]

how can i filter for significant hits? and how can i collect the ids of query sequences with a significant hits? can you share grep command for it?