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,
I have a fasta file as follows,
gene.fasta
The expected output should be like this,
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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LEARN ABOUT DEBIAN
colorgccrc
COLORGCCRC(5) File Formats Manual COLORGCCRC(5)NAME
colorgccrc - configuration file for colorgcc
DESCRIPTION
A colorgccrc configuration file is used to configure the highlighting of the compiler output from colorgcc.
SYNTAX
Each line consists of a keyword designating a configuration variable. The keyword is followed by `:' and then one or several values
(depending on the keyword). Lines beginning with a hash mark `#' are comments.
CONFIGURATION VARIABLES
g++ | gcc | c++ | cc | g77 | gcj | gnat | gpc
Specifies the paths to the compilers. Takes one value; a path to the compiler.
nocolor
Specifies what terminal types colorization should be disabled on. Takes one or several values, separated by whitespace.
srcColor
Specifies the highlighting attributes source-code should be given. Takes one or several color attributes. See the section COLOR
ATTRIBUTES for more information.
introColor
Specifies the highlighting attributes for normal compiler output. Takes one or several color attributes. See the section COLOR
ATTRIBUTES for more information.
warningFileNameColor | errorFileNameColor
Specifies the highlighting attributes for the filename in a warning or an error, respectively. Takes one or several color
attributes. See the section COLOR ATTRIBUTES for more information.
warningNumberColor | errorNumberColor
Specifies the highlighting attributes for the line-number in a warning or an error, respectively. Takes one or several color
attributes. See the section COLOR ATTRIBUTES for more information.
warningMessageColor | errorMessageColor
Specifies the highlighting attributes for the message-text in a warning or an error, respectively. Takes one or several color
attributes. See the section COLOR ATTRIBUTES for more information.
COLOR ATTRIBUTES
The following attributes are valid for highlighting.
clear, reset
bold, underline, underscore, blink, reverse, concealed
black, red, green, yellow, blue, magenta, cyan, white
on_black, on_red, on_green, on_yellow, on_blue, on_magenta, on_cyan, on_white
SEE ALSO gcc(1), colorgcc(1)HISTORY
Jan 15 2003: Initial version of this manual-page.
REPORTING BUGS
Report bugs to <jmoyers@geeks.com>
AUTHORS
Jamie Moyers <jmoyers@geeks.com> is the author of colorgcc.
This manual page was written by Joe Wreschnig <piman@sacredchao.net>, and modified by David Weinehall <tao@debian.org>, for the Debian
GNU/Linux system (but may be used by others).
COPYRIGHT
Copyright (C) 2003 Jamie Moyers
This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICU-
LAR PURPOSE.
Jan 15, 2003 COLORGCCRC(5)