ArchTEx: accurate extraction and visualization of next-generation sequence data.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 22302569.
- Also identified by DOI 10.1093/bioinformatics/bts063.
- No licence information is recorded for this record.
- Because redistribution is not established, this page shows the abstract only. Follow the links below for the full text.
Abstract
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. ArchTEx requires Java 1.6 or newer. Source code and the compiled program are freely available at http://sourceforge.net/projects/archtex/ mjbuck@buffalo.edu Supplementary data are available at Bioinformatics online.
Medical subject headings
- Algorithms
- Computational Biology
- Expressed Sequence Tags
- Sequence Analysis, DNA
- Software