:: DESCRIPTION
SMRT Analysis is a bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data from Pacific Biosciences.
::DEVELOPER
Pacific Biosciences of California, Inc
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Integr. 2011 Dec 20;2:10. doi: 10.1186/2041-9414-2-10.
Direct detection and sequencing of damaged DNA bases.
Clark TA, Spittle KE, Turner SW, Korlach J.
:: DESCRIPTION
Scalpel is a software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology .
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Accurate de novo and transmitted indel detection in exome-capture data using microassembly.
Narzisi G, O’Rawe JA, Iossifov I, Fang H, Lee YH, Wang Z, Wu Y, Lyon GJ, Wigler M, Schatz MC.
Nat Methods. 2014 Oct;11(10):1033-6. doi: 10.1038/nmeth.3069.
:: DESCRIPTION
DELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
DELLY: structural variant discovery by integrated paired-end and split-read analysis
Tobias Rausch; Thomas Zichner; Andreas Schlattl; Adrian M. Stütz; Vladimir Benes; Jan O. Korbel
Bioinformatics 2012 28: i333-i339
:: DESCRIPTION
The DiNAMO software implements an exhaustive algorithm to detect over-represented IUPAC motifs in a set of DNA sequences. It has two modes: scanning mode, where all windows are parsed, or fixed-position mode, where only motifs occurring at a specific position in the sequences are taken into account.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Saad C, Noé L, Richard H, Leclerc J, Buisine MP, Touzet H, Figeac M.
DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data.
BMC Bioinformatics. 2018 Jun 11;19(1):223. doi: 10.1186/s12859-018-2215-1. PMID: 29890948; PMCID: PMC5996464.
:: DESCRIPTION
Dendrix (De novo Driver Exclusivity) is an algorithm for discovery of mutated driver pathways in cancer using only mutation data. It finds sets of genes, domains, or nucleotides whose mutations exhibit both high coverage and high exclusivity in the analyzed samples.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
F. Vandin, E. Upfal, B.J. Raphael. (2011)
De novo Discovery of Mutated Driver Pathways in Cancer.
Genome Res. 2011 Jul 11
:: DESCRIPTION
MultiFinder performs automated motif searching using four different profile-based motif finders, including AlignACE, MDscan, BioProspector and MEME.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2006 Apr 27;7:229.
Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data.
Huber BR, Bulyk ML.
:: DESCRIPTION
VirusSeeker is a set of fully automated and modular software package designed for mining next generation sequencing data form Illumina platform to identify sequences of viral origin.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Zhao G, Wu G, Lim ES, Droit L, Krishnamurthy S, Barouch DH, Virgin HW, Wang D.
VirusSeeker, a computational pipeline for virus discovery and virome composition analysis.
Virology. 2017 Mar;503:21-30. doi: 10.1016/j.virol.2017.01.005. Epub 2017 Jan 18. PMID: 28110145; PMCID: PMC5326578.
:: DESCRIPTION
COSSY is an algorithm to discover important subnetworks differentiating between two phenotypes (context). It automatically finds differentially expressed subnetworks of closely interacting molecules from molecular interaction networks (such as KEGG or STRING) using gene expression profiles. This is the first non-greedy approach of its kind. COSSY works for any interaction network regardless of the network topology. It can also be used as a highly accurate classification platform.
::DEVELOPER
Data Mining & Information Systems Lab, TAN LAB
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Saha A, Tan AC, Kang J.
Automatic context-specific subnetwork discovery from large interaction networks.
PLoS One. 2014 Jan 1;9(1):e84227. doi: 10.1371/journal.pone.0084227. PMID: 24392115; PMCID: PMC3877685.
:: DESCRIPTION
BioPlat (Biomarkers Platform) is a user-friendly bioinformatic resource, which provides a set of analytic tools and predefined pipelies for the discovery and in silico evaluation of novel prognostic and predictive cancer biomarkers based on integration of different genomics data profiles and re-use of gene expression signature in the context of follow-up data.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Jun 15;30(12):1782-4. doi: 10.1093/bioinformatics/btu111. Epub 2014 Feb 25.
BioPlat: a software for human cancer biomarker discovery.
Butti MD, Chanfreau H, Martinez D, García D, Lacunza E, Abba MC.
:: DESCRIPTION
MAQGene is a software for C. elegans biologists with next-gen sequence data, facilitates genome-wide discovery of biologically meaningful mutations.MAQGene classifies each found mutation based on its canonically predicted effect on the coding sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nat Methods. 2009 Aug;6(8):549. doi: 10.1038/nmeth.f.260.
MAQGene: software to facilitate C. elegans mutant genome sequence analysis.
Bigelow H, Doitsidou M, Sarin S, Hobert O.
