I have whole proteome data-set (Fasta files. txt) of wheat and need to run on various bioinformatics programs (For this I need proteins with more than 50 amino acids). How I can filter/ delete the peptide sequences with less than 50 amino acids from whole proteome dataset? May be some programming expert could help!
I think that I can help you, but I don't know, how is your fasta.
Can you show me?
I use the script linked below to filter sequences by size in multifasta files.
http://raven.iab.alaska.edu/~ntakebay/teaching/programming/perl-scripts/selectSeqs.pl
This bash shell script may help.
more fasta_file | awk '{if ($0 ~ /^>/) print "#"$0"#";else print $0"#\t"length($0) }' | tr -d '\n' | sed "s/#>/\n>/g" | awk '{if ($2 > 50) print $0}' | awk '{print $1}' | tr '#' '\n' | grep -v "^$"
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