Suffix tree searcher: exploration of common substrings in large DNA sequence sets.

ABSTRACT:

Background

Large DNA sequence data sets require special bioinformatics tools to search and compare them. Such tools should be easy to use so that the data can be easily accessed by a wide array of researchers. In the past, the use of suffix trees for searching DNA sequences has been limited by a practical need to keep the trees in RAM. Newer algorithms solve this problem by using disk-based approaches. However, none of the fastest suffix tree algorithms have been implemented with a graphical user interface, preventing their incorporation into a feasible laboratory workflow.

Results

Suffix Tree Searcher (STS) is designed as an easy-to-use tool to index, search, and analyze very large DNA sequence datasets. The program accommodates very large numbers of very large sequences, w

SUBMITTER: Minkley D 

PROVIDER: S-EPMC4118789 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature