BOL

I don't have any code for you, but you can find several useful links here http://bioinformaticsonline.com/bookmarks/view/4098/bioinformatics-algorithm-demonstrations-and-tutorials which might help you to resolve the problems.

Note: If you are not able to view this, it means you need to join http://bioinformaticsonline.com/groups/profile/4030/bioinformatics-algorithms group first.

Thanks
Rahul

If you don't mind using BioPerl, you can try Bio::Tools::SeqPattern module for this purpose http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/SeqPattern.html

Hope helpful.

Best
Shreya

Hi Shyam,

Please find one of my perl code to extract matching string region at http://bioinformaticsonline.com/file/view/4882/detect-the-sequence-pattern-and-its-location-in-fasta-file-with-match-and-mismatches-information

Hopefully this will be useful for your pattern searching stuff.

Thanks
Jit

If you are only looking for string matching algorithms to implements then this notes will be much useful for you. http://users.csc.calpoly.edu/~dekhtyar/448-Spring2013/lectures/lec05.448.pdf

http://www.math-info.univ-paris5.fr/~nuel/lecture_main_algo.pdf

The tutorial http://www.catalysoft.com/articles/StrikeAMatch.html sounds like it may be perfect for your need.

The edit-distance algorithm is the standard algorithm for dictionary match suggestions, and can work on whole texts. http://www.norvig.com/spell-correct.html

Best of luck.

Cheers

Some other Fast and Exact String Pattern-matching Algorithms for further reading:

http://www.cs.otago.ac.nz/cosc348/alignments/Lecture04_StringSearch.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC61442/

http://bioinformatics.oxfordjournals.org/content/17/suppl_1/S207.full.pdf

http://www.eui.upm.es/~fmartin/webpgomez/Docencia/Pattern-Recognition/PR-Notes-Chapter-3.pdf

String Matching Evaluation Methods for DNA Comparison
http://www.sersc.org/journals/IJAST/vol47/2.pdf

Cheers

Hi Shyam,

There are several algorithms applied for pattern searching, please find the introduction at http://orion.lcg.ufrj.br/Dr.Dobbs/books/book5/chap10.htm

Cheers