MOTIVATION: 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. AVAILABILITY AND IMPLEMENTATION: ArchTEx requires Java 1.6 or newer. Source code and the compiled program are freely available at http://sourceforge.net/projects/archtex/ CONTACT: mjbuck@buffalo.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: 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. AVAILABILITY AND IMPLEMENTATION: ArchTEx requires Java 1.6 or newer. Source code and the compiled program are freely available at http://sourceforge.net/projects/archtex/ CONTACT: mjbuck@buffalo.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Yad Ghavi-Helm; Felix A Klein; Tibor Pakozdi; Lucia Ciglar; Daan Noordermeer; Wolfgang Huber; Eileen E M Furlong Journal: Nature Date: 2014-07-02 Impact factor: 49.962
Authors: Robert M Givens; William K M Lai; Jason M Rizzo; Jonathan E Bard; Piotr A Mieczkowski; Janet Leatherwood; Joel A Huberman; Michael J Buck Journal: Nucleic Acids Res Date: 2012-05-09 Impact factor: 16.971