Hello All,

How to Grep only specific motif from complete sequences in a fasta file using shell command? Also, I want to include the lines beginning with a > before these target sequences. I got help from the previous post in this link: A: grep whole sequences containing a specific motif in a fasta file to grep whole sequence containing motifs but now I want to grep only motifs with protein id as a header. Some protein sequence has more than one motifs.

My motifs look like that : SXXXX(F/S)XXXL

Here are list of protein sequences

sp|Q9H257.2|CARD9_HUMAN RecName: Full=Caspase recruitment domain-containing protein 9; Short=hCARD9 MSDYENDDECWSVLEGSRVTLTSVIDRSRITPYLRQTKVLNPDDEEQVLSDPNLSIRKRKVGVLLDILQRTGHKGYVAFLESLELYYPQLYKKVTGKEPARVFSMIIDASGESGLTQLLMSEVMWFLQKLVQDLTALLSSK

sp|Q9H37.2|CTYU_HUMAN HHHSVLEGFRVTLTSVIDRFRITPYLRQTKVLNPDDEEQVLSDPNLVIRKRKVGVLLDILQRTGHKGYVAFLESLELYYPQLYKKVTGKEPARVFSMIIDASGESYSLTQLLMTEVMKLQKKVQDLTALLSSK

sp|Q9re7.2|CARer_HUMAN RecName BKLSVLEGWRVTLTSVIDRFRITPYLRQTKVLNPDDEEQVLSDPNLVIRKRKVGVLLDILQRTGHKGYVAFLESLELYYPQLYKKVTGKEPARVFSMIIDASGESGLTQLLMTEVMKLQKKVQDLTALLSSK

Result should be displayed like:

sp|Q9H257.2|CARD9_HUMAN RecName: Full=Caspase recruitment domain-containing

SVLEGSRVTL

sp|Q9H257.2|CARD9_HUMAN RecName: Full=Caspase recruitment domain-containing

SEVMWFLQKL

sp|Q9H37.2|CTYU_HUMAN

SVLEGFRVTL

sp|Q9H37.2|CTYU_HUMAN

SGESSLTQL