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Full Discussion: Help with finding matching position on strings
Top Forums UNIX for Dummies Questions & Answers Help with finding matching position on strings Post 302507273 by pawannoel on Wednesday 23rd of March 2011 11:05:21 AM
Old 03-23-2011
Lightbulb Help with finding matching position on strings
I have a DNA file like below and I am able to write a short program which finds/not an input motif, but I dont understand how I can include in the code to report which position the motif was found. Example I want to find the first or all "GAT" motifs and want the program to report which position (beginning to end) of the dna motif was found. So in this example GAT (in bold should report 10-12) and if found more than once the other positions too. Can someone explain how to report matching position on strings ??

Thank you very much

Code:
>MY_DNA  
CAGCAGCAAGATTTGCAGCAACAGCAACAAGTAGTGACTACAGTTGCCTCGCAAAGTCCT
CATGCAACTGCAACGGAAAAGGAGCCAGTACCCGCCGTGGTTGACGACCCACTGGAGAAC
ATGTTCGGAGATTATTCCAATGAGCCGTTCAACACCAATTTCGACGATGAATTTGGAGAT

 

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LEARN ABOUT DEBIAN

glam2scan

GLAM2SCAN(1)							   glam2 Manual 						      GLAM2SCAN(1)

NAME

       glam2scan - finds a GLAM2 motif in a database

SYNOPSIS

       glam2scan [options] alphabet my_motif.glam2 my_seqs.fa

       An alphabet other than p or n is interpreted as the name of an alphabet file.

DESCRIPTION

       glam2scan finds matches, in a sequence database, to a motif discovered by glam2. Each match receives a score, indicating how well it fits
       the motif.

OPTIONS (DEFAULT SETTINGS)
       -h
	   Show all options and their default settings.

       -o
	   Output file (stdout).

       -n
	   Number of alignments to report (25).

       -2
	   Examine both strands - forward and reverse complement.

       -D
	   Deletion pseudocount (0.1).

       -E
	   No-deletion pseudocount (2.0).

       -I
	   Insertion pseudocount (0.02).

       -J
	   No-insertion pseudocount (1.0).

       -d
	   Dirichlet mixture file.

SEE ALSO

       glam2format(1), glam2mask(1), glam2-purge(1), glam2(1)

       The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in
       /usr/share/doc/glam2/.

REFERENCE

       If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and
       deletions, PLoS Computational Biology (in press).

AUTHORS

       Martin Frith
	   Author of GLAM2.

       Timothy Bailey
	   Author of GLAM2.

       Charles Plessy <plessy@debian.org>
	   Formatted this manpage in DocBook XML for the Debian distribution.

COPYRIGHT

       The source code and the documentation of GLAM2 are released in the public domain.

GLAM2 1056							    05/19/2008							      GLAM2SCAN(1)
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