Extract sequences which do not have blast hits

Question

[karthic]

Hi,

I have a fasta file with around 1 million sequences. I did a blast search and got hits for around 7500 sequences. Now I want to extract those sequences which do not have a hit and take them for further analysis.

So far am using a custom sed script which is very slow, judging from the speed, it might take several days to complete. Please help me with fast and robust solutions.

the script am using currently is below..

    cat CG061MR_S20_R1_001_AR_filter_un_ren.fa > CG061MR_S20_R1_001_AR_filter_unblasted.fa

    for j in $(cat CG061MR_blastids.txt)    
    do
    sed -i -e '/'$j'/{N;d}' CG061MR_S20_R1_001_AR_filter_unblasted.fa

done

Thank You KK

Answer 1

[karthic]

Sorry guys for bothering.

Found the solution with Jim kent's faSomeRecords

Thank You

KK

[cpad0112]

faSomeRecords or GetFaRecords? karthic

[karthic]

Sorry, its faSomeRecords. Corrected it.