ArchTEx: accurate extraction and visualization of next-generation sequence data | Zendy

William Lai | Zendy; Jonathan Bard | Zendy; Michael Buck | Zendy

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ArchTEx: accurate extraction and visualization of next-generation sequence data

Author(s) -

William Lai,

Jonathan Bard,

Michael Buck

Publication year - 2012

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bts063

Subject(s) - computer science , extension (predicate logic) , source code , sequence (biology) , java , visualization , data mining , code (set theory) , data extraction , programming language , information retrieval , biology , biochemistry , genetics , set (abstract data type) , medline

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.

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