grep only specific motif from whole protein sequence

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

This command will take the whole sequence that contains motif I don't want to do like that

grep -E 'S[A-Z]{4}[FS][A-Z]{3}L' jara3.fasta > jara4.fasta

sequencing

• 1,451 views • link

updated 7.9 years ago by Pierre Lindenbaum

• written 7.9 years ago by Jason •

I added markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

101010 Button

• 1 views • link

written 7.9 years ago by WouterDeCoster

Hello Jason!

We believe that this post does not fit the main topic of this site.

Pure unix question, a man grep is all it'll take to get to your answers, which involves grep -o. Or better, use bioawk

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

• 1 views • link

written 7.9 years ago by Ram

The answer is in the first hits if you google grep only print matching pattern

• 1 views • link

written 7.9 years ago by WouterDeCoster

1 answer

 cat input.fa | paste - - | awk -F '\t' '{N=match($2,/(S....[FS]...L)/,a);if(N==0) next;printf("%s\n%s\n",$1,a[1]);}'

>sp|Q9H257.2|CARD9_HUMAN RecName: Full=Caspase recruitment domain-containing protein 9; Short=hCARD9
SVLEGSRVTL
>sp|Q9H37.2|CTYU_HUMAN 
SVLEGFRVTL

(assuming two lines par fasta record. Otherwise, use https://gist.github.com/lindenb/2c0d4e11fd8a96d4c345 )

• 1 views • link

written 7.9 years ago by Pierre Lindenbaum

Hey, Thanks for help but I'm getting error. How can I resolve it

awk: syntax error at source line 1

context is

>>> {N=match($2,/(S....[FS]...L)/, <<< 
awk: illegal statement at source line 1
awk: illegal statement at source line 1

• 1 views • link

updated 7.9 years ago by Ram

• written 7.9 years ago by Jason •

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

• 1 views • link

written 7.9 years ago by Ram

$ awk --version
GNU Awk 4.1.3, API: 1.1 (GNU MPFR 3.1.4, GNU MP 6.1.0)
Copyright (C) 1989, 1991-2015 Free Software Foundation.

• 1 views • link

written 7.9 years ago by Pierre Lindenbaum