:: DESCRIPTION
samblaster is a tool to mark duplicates and extract discordant and split reads from sam files.
::DEVELOPER
Greg Faust (gf4ea@virginia.edu)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2014 May 7. [Epub ahead of print]
SAMBLASTER: fast duplicate marking and structural variant read extraction.
Faust GG1, Hall IM.
:: DESCRIPTION
CHEXVIS is a tool for molecular channel extraction and visualization. CHEXVIS supports the visual exploration of multiple channels together with their geometric and physico-chemical properties thereby enabling the understanding of the basic biology of transport through protein channels
::DEVELOPER
Visualization & Graphics Lab, Dept. of Computer Science & Automation, and Chandra Lab, Dept. of Biochemistry.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
CHEXVIS: a tool for molecular channel extraction and visualization
Masood TB, Sandhya S, Chandra N, Natarajan V.
BMC Bioinformatics. 2015 Apr 16;16(1):119.
:: DESCRIPTION
miRTex is a text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature.
::DEVELOPER
Center for Bioinformatics and Computational Biology, University of Delaware
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
miRTex: A Text Mining System for miRNA-Gene Relation Extraction.
Li G, Ross KE, Arighi CN, Peng Y, Wu CH, Vijay-Shanker K.
PLoS Comput Biol. 2015 Sep 25;11(9):e1004391. doi: 10.1371/journal.pcbi.1004391.
:: DESCRIPTION
V-Xtractor is a Perl-based, high-throughput software tool that locates, verifies, and extracts defined segments of sequence information from sequence datasets. Hidden Markov Models are used to detect the conserved boundaries of the target region and to extract the interjacent sequence information (that is for example the hyper-variable regions of the rRNA gene or the internal transcribed spacer regions of the rRNA operon). This tool extracts phylogenetically comparable regions without prior multiple sequence alignments and improves reliability of the data by confirming basic authenticity of the sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hartmann M, Howes CG, Abarenkov K, Mohn WW, Nilsson RH (2010).
V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences.
Journal of Microbiological Methods 83(2): 250-253.
:: DESCRIPTION
EDGE is a software package for the significance analysis of DNA microarray experiments for both standard and time course experiments based on our new Optimal Discovery Procedure and Time Course Methodology
::DEVELOPER
Jeffrey Leek, Alan Dabney, Eva Monsen and John Storey.
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Feb 15;27(4):509-15. doi: 10.1093/bioinformatics/btq701. Epub 2010 Dec 24.
A computationally efficient modular optimal discovery procedure.
Woo S, Leek JT, Storey JD.
:: DESCRIPTION
ACME (Advanced parallel motif extractor) is an advanced parallel motif extractor. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Majed Sahli, Essam Mansour, Panos Kalnis:
ACME: Efficient Parallel Motif Extraction from Very Long Sequences.
Technical Report
:: DESCRIPTION
ITSx is a software tool for detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing
Johan Bengtsson-Palme, Vilmar Veldre, Martin Ryberg, Martin Hartmann, Sara Branco, Zheng Wang, Anna Godhe, Yann Bertrand, Pierre De Wit, Marisol Sanchez, Ingo Ebersberger, Kemal Sanli, Filipe de Souza, Erik Kristiansson, Kessy Abarenkov, K. Martin Eriksson, R. Henrik Nilsson
Methods in Ecology and Evolution, 2013
:: DESCRIPTION
XSTREAM is a rapid and powerful algorithm for identifying perfect and degenerate tandem repeat motifs in protein (and nucleotide) sequence data. XSTREAM also effectively models the architecture of repetitive domains in tandem repeat proteins and eliminates motif redundancy to identify “fundamental” tandem repeat patterns.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2007 Oct 11;8:382.
XSTREAM: a practical algorithm for identification and architecture modeling of tandem repeats in protein sequences.
Newman AM, Cooper JB.
:: DESCRIPTION
metaRNAmodules is a pipeline which completely automates extracting putative FR3D modules and mapping of such modules to Rfam alignments to obtain comparative evidence.
::DEVELOPER
Center for non-coding RNA in Technology and Health (RTH)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2013 Dec;41(22):9999-10009. doi: 10.1093/nar/gkt795.
Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.
Theis C, Höner Zu Siederdissen C, Hofacker IL, Gorodkin J.
:: DESCRIPTION
MoTeX is an accurate and efficient tool for MoTif eXtraction.
:: DEVELOPER
Dr. Solon P. Pissis
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Solon P. Pissis, Alexandros Stamatakis, and Pavlos Pavlides.
MoTeX: a word-based HPC tool for MoTif eXtraction.
the Fourth ACM International Conference on Bioinformatics and Computational Biology (ACM-BCB 2013), pp. 13-22, 2013. ACM Digital Library