Step 6: Extraction of sequences from fasta file using fastacmd

To extract subset of sequences from Lycopersicon_esculentum.fasta file fastacmd (included with NCBI BLAST stand alone distribution) program has been used:

$ fastacmd -d Lycopersicon_esculentum.fasta -i Lycopersicon_esculentum.with_hits.IDs -o Lycopersicon_esculentum.with_hits.fasta

Then fasta headers of Lycopersicon_esculentum.with_hits.fasta file have been modified using perl (/find/replace/) regular expression:

$ perl -p -i -e 's/^\>lcl\|/\>/' Lycopersicon_esculentum.with_hits.fasta



So far, we have reduced number of ESTs in Lycopersicon esculentum set from 150193 to 32887.