ArchTEx: accurate extraction and visualization of next-generation sequence data.
BACKGROUND
The extension of mapped sequence tags is a common step in the analysis of single-end next-generation sequencing (NGS) data from protein localization and chromatin studies. The optimal extension can vary depending on experimental and technical conditions. Improper extension of sequence tags can obscure or mislead the interpretation of NGS results. We present an algorithm, ArchTEx (Architectural Tag Extender), which identifies the optimal extension of sequence tags based on the maximum correlation between forward and reverse tags and extracts and visualizes sites of interest using the predicted extension.


METHODS
ArchTEx requires Java 1.6 or newer. Source code and the compiled program are freely available at http://sourceforge.net/projects/archtex/


BACKGROUND
mjbuck@buffalo.edu


BACKGROUND
Supplementary data are available at Bioinformatics online.
Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14203, USA.
William K M
WK
Lai
Jonathan E
JE
Bard
Michael J
MJ
Buck
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D020224:Expressed Sequence Tags; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software