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Full Discussion: How to find a specific sequence pattern in a fasta file?
Top Forums UNIX for Beginners Questions & Answers How to find a specific sequence pattern in a fasta file? Post 303041608 by dineshkumarsrk on Friday 29th of November 2019 03:56:12 AM
Old 11-29-2019
How to find a specific sequence pattern in a fasta file?
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
Code:
AAGCZ-N16-AAGCZ
Z represents A, C or G (Except T)
N16 represents any of the four bases including A, T, G or C and these four base combination should have the length of 16 bases.

I have a fasta file as follows,
gene.fasta
Code:
>dox
ATGCTATGATAGTAGTAGATAGAGAGAGAGATAGATAGAGAGATAGATAG
>cyclin
ATGAGATAGAAAGCCATAGATAGTAGTAGATAAGCATATAGATAGATAGTAGTGATA
>fyl
TAGTAGTAGATAGATAGATGCGTACTGCTGATGATAGATGATAGATAGATAGATTAGAT
>tubulin
TAGATAGAAAGCAATAGATAGAACAAGATAAGCCTAGTCGTAGATGATAGATAG

The expected output should be like this,
Code:
>org1_1
ATAGAAAGCCATAGATAGTAGTAGATAAGCATATAG
>org1_2
ATAGAAAGCAATAGATAGAACAAGATAAGCCTAGTC

In order to mine the above mentioned pattern, I have used grep command but, I do not know how to specify only 3 bases for Z and also I could not specify N16 criteria in the grep command line. In addition to this, I do not know how to mine the 5 of the flanking bases along with the pattern. So kindly help me in this regard.
Thank you in advance.
Last edited by dineshkumarsrk; 11-29-2019 at 07:15 AM..
 

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gchem3d

GCHEM3D(1)						       gnome-chemistry-utils							GCHEM3D(1)

NAME

       gchem3d - a small chemical viewer application

SYNOPSIS

       gchem3d [OPTION(S)...] [FILE...]

DESCRIPTION

       gchem3d is a small chemical viewer application, which can show several chemical file formats.

OPTIONS

       The following options are accepted:

       -b COLOR, --bgcolor=COLOR
	   Use the given color as background color.  COLOR can be one of "black" (default), "white", "#rrggbb" (don't forget to escape the "#"
	   character in the shell).

       -d MODEL, --display3d=MODEL
	   Choose how molecules are displayed.	MODEL can be one of "BallnStick" (default), "SpaceFill".

       -?, --help
	   Show application help options.

       --help-all, --help-*
	   Print all or just a group of help options. These options are not documented here. Instead see gtk-options(7) and gnome-options(7).

       -v, --version
	   Print gchem3d version information.

SEE ALSO

       gnome-options(7), gtk-options(7)

AUTHORS

       Jean Brefort <jean.brefort@normalesup.org>
	   Program author.

       Daniel Leidert <daniel.leidert@wgdd.de>
	   Manpage author.

COPYRIGHT

       Copyright (C) 2002-2007 Jean Brefort
       Copyright (C) 2004-2007 Daniel Leidert

       Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or any
       later version published by the Free Software Foundation.

gcu 0.12				      $Date: 2009-03-19 10:53:47 +0100 (jeu. 19 mars 2009) $					GCHEM3D(1)
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