Optimus Primer – Primer Design for large-scale Resequencing by Second Generation Sequencing

Optimus Primer

:: DESCRIPTION

Optimus Primer is a PCR enrichment primer design program for next-generation sequencing of human exonic regions.

::DEVELOPER

Laboratory of Guillaume Lettre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Res Notes. 2010 Jul 7;3:185. doi: 10.1186/1756-0500-3-185.
Optimus Primer: A PCR enrichment primer design program for next-generation sequencing of human exonic regions.
Brown AM, Lo KS, Guelpa P, Beaudoin M, Rioux JD, Tardif JC, Phillips MS, Lettre G.

RESQUE 1.0 – REduction-based scheme using Semi-Markov scores for networkQUEing

RESQUE 1.0

:: DESCRIPTION

RESQUE is an efficient algorithm for querying large-scale biological networks.

::DEVELOPER

Mohammad Ebrahim Sahraeian and Byung-Jun Yoon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Python / Matlab

:: DOWNLOAD

RRESQUE

:: MORE INFORMATION

Citation

RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon,
Bioinformatics, 28 (16): 2129-2136, 2012. doi:10.1093/bioinformatics/bts341

PASH 3.0.6.2 – Large-scale Sequence Comparison Method

PASH 3.0.6.2

:: DESCRIPTION

PASH is an efficient large-scale sequence comparison method that uses positional hashing.

::DEVELOPER

Bioinformatics Research Laboratory, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
C++ Compiler

:: DOWNLOAD

PASH

:: MORE INFORMATION

Citation

Coarfa C, Yu F, Miller CA, Chen Z, Harris RA, Milosavljevic A.
Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing.
BMC Bioinformatics. 2010 Nov 23;11:572

CpGpromoter – Large-scale Human Promoter Mapping using CpG islands

CpGpromoter

:: DESCRIPTION

CpGpromoter is a program for a large-scale human promoter mapping using CpG islands. As defined by Gardiner-Garden & Frommer, CpG islands are greater than 200 bp in length, have more than 50% of G+C content, and have a CpG frequency of at least 0.6 of that expected on the basis of the G+C content of the region. CpG islands are an important signature of 5′ region of many mammalian genes. The program is based on results of discriminant analysis between the promoter-associated CpG islands and non-associated ones (Ioshikhes & Zhang). It enables an efficient mapping of human promoters with 2Kb resolution, if there is a CpG island inside an interval (-500…+1,500) around a transcription start site (TSS).

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Ioshikhes, I. & Zhang, M.Q.
Large-scale human promoter mapping using CpG islands.
Nature Genetics 26, 61-63 (2000)

GADEM 1.3.1 – Motif Discovery tool for Large-scale Genomic Sequence data

GADEM 1.3.1

:: DESCRIPTION

GADEM is an unbiased de novo motif discovery tool implementing an expectation-maximization (EM) algorithm.

::DEVELOPER

Leping Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GADEM

:: MORE INFORMATION

Citation:

Li L.
GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery.
J Comput Biol. 2009 Feb;16(2):317-29.

GS-Aligner 1.0 – Large-scale Pairwise Sequence Alignment

GS-Aligner 1.0

:: DESCRIPTION

GS-Aligner that uses bit-level operations was developed for aligning genomic sequences. GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions. It is suitable for aligning fairly divergent sequences such as human and mouse genomic sequences. It consists of several efficient components: bit-level coding, search for matching segments between the two sequences as alignment anchors, longest increasing subsequence (LIS), and optimal local alignment. Efforts have been made to reduce the execution time of the program to make it truly practical for aligning very long sequences. Empirical tests suggest that for relatively divergent sequences such as sequences from different mammalian orders or from a mammal and a nonmammalian vertebrate GS-Aligner performs better than existing methods.

::DEVELOPER

Chun-Chieh Shih and Wen-Hsiung Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GS-Aligner

:: MORE INFORMATION

Citation:

GS-Aligner: A Novel Tool for Aligning Genomic Sequences Using Bit-Level Operations
Chun-Chieh Shih and Wen-Hsiung Li
Mol Biol Evol (2003) 20 (8): 1299-1309.

Vmatch – Large Scale Sequence Analysis Software

Vmatch

:: DESCRIPTION

Vmatch is a versatile software tool for efficiently solving large scale sequence matching tasks. Vmatch subsumes the software tool REPuter, but is much more general, with a very flexible user interface, and improved space and time requirements.

::DEVELOPER

Stefan Kurtz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

Vmatch

:: MORE INFORMATION

If you need Vmatch for an additional platform, then please contact Stefan Kurtz. If you want to use Vmatch for academic research, educational and demonstration purposes you may obtain a free of charge non-commercial license as follows: download the license agreement form, read it, sign it, and fax it to the number given in the agreement. If you want to obtain a commercial license for Vmatch, then please directly contact Stefan Kurtz

GNLab -Computational Pipeline for Large-Scale Gene Network Analysis

GNLab

:: DESCRIPTION

GNLab (Gene Network virtual Laboratory) is a novel bioinformatics tool for the large-scale analysis of gene regulatory networks (GRNs). This C++ command-line tool supports the analysis of both the static structure and dynamic behaviour of a GRN. GNLab is developed to support the design and implementation of large-scale repeatable computational experimentations on GRNs.

::DEVELOPER

Joshua Ho , University of Sydney,

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

GNLab

:: MORE INFORMATION

License