MaxSSmap v1 – GPU program for Mapping Divergent Short Reads to Genomes with the Maximum Scoring Subsequence

MaxSSmap v1

:: DESCRIPTION

MaxSSmap is a GPU program with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. MaxSSmap identifies a local region of the genome followed by exact alignment.

::DEVELOPER

Usman Roshan

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux

:: DOWNLOAD

MaxSSmap

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Nov 15;15:969. doi: 10.1186/1471-2164-15-969.
MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence.
Turki T1, Roshan U.

MSS 1.0 – Finding all Maximal Scoring Subsequences

MSS 1.0

:: DESCRIPTION

MSS (Maximal Scoring Subsequences) is a practical, linear time algorithm to find, in a sequence of numeric scores, those nonoverlapping, contiguous subsequences having greatest total scores.

::DEVELOPER

The Computational & Synthetic Biology group – COMPUTER SCIENCE & ENGINEERING at UNIVERSITY OF WASHINGTON

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

MSS Source Code

:: MORE INFORMATION

Citation:

W. Ruzzo, M. Tompa, “A linear time algorithm for finding all maximal scoring subsequences”, Proc Int Conf Intell Syst Mol Biol, (1999) 234-41. Pubmed 10786306.