GNU Pattern: open source pattern hunter for biological sequences based on SPLASH algorithm.

Author: Ying XU ¹ ; Yi-xue LI ; Xiang-yin KONG
Author Information

1. Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, China.
Publication Type:Journal Article
MeSH: Algorithms; Computational Biology; Pattern Recognition, Automated; Sequence Analysis, DNA; Software
From: Acta Academiae Medicinae Sinicae 2005;27(3):265-269
CountryChina
Language:Chinese
Abstract:
OBJECTIVETo construct a high performance open source software engine based on IBM SPLASH algorithm for later research on pattern discovery.
METHODSGpat, which is based on SPLASH algorithm, was developed by using open source software.
RESULTSGNU Pattern (Gpat) software was developped, which efficiently implemented the core part of SPLASH algorithm. Full source code of Gpat was also available for other researchers to modify the program under the GNU license.
CONCLUSIONGpat is a successful implementation of SPLASH algorithm and can be used as a basic framework for later research on pattern recognition in biological sequences.