ExomeCopy 1.32.0 – Copy Number Variant Detection from Exome Sequencing Read Depth

ExomeCopy 1.32.0

:: DESCRIPTION

ExomeCopy implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

::DEVELOPER

Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 ExomeCopy

:: MORE INFORMATION

Citation

Stat Appl Genet Mol Biol. 2011 Nov 8;10(1).
Modeling read counts for CNV detection in exome sequencing data.
Love MI, Myšičková A, Sun R, Kalscheuer V, Vingron M, Haas SA.

PASTAA – Detecting Transcriptions Factors Associated with Functional Categories

PASTAA

:: DESCRIPTION

PASTAA is a software for detecting transcriptions factors associated with functional categories, which utilizes the prediction of binding affinities of a TF to promoters. This binding strength information is compared to the likelihood of membership of the corresponding genes in the functional category under study. Coherence between the two ranked datasets is seen as an indicator of association between a TF and the category. PASTAA is applied primarily to the determination of TFs driving tissue-specific expression.

::DEVELOPER

the Computational Molecular Biology Department at the Max Planck Institute for Molecular Genetics in Berlin, Germany.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 PASTAA

:: MORE INFORMATION

Citation

Helge G. Roider*, Thomas Manke, Sean O’Keeffe, Martin Vingron and Stefan A. Haas
PASTAA: identifying transcription factors associated with sets of co-regulated genes
Bioinformatics (2009) 25 (4): 435-442.

FFN – Finding Features for Nucleosomes

FFN

:: DESCRIPTION

FFN is a pattern discovery and scoring algorithm to identify feature patterns that are differentially enriched in nucleosome-forming sequences and nucleosome-depletion sequences

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 FFN

:: MORE INFORMATION

Citation:

Genomics. 2014 Jul 23. pii: S0888-7543(14)00117-7. doi: 10.1016/j.ygeno.2014.07.002. [Epub ahead of print]
Computational discovery of feature patterns in nucleosomal DNA sequences.
Zheng Y, Li X, Hu H

MBBC 1.1 – Metagenomic Binning Based on Composition

MBBC 1.1

:: DESCRIPTION

MBBC is a useful tool in metagenomic studies. It is a novel composition-based approach to bin environmental shotgun reads, by considering the k-mer frequency in reads and the inferred Markovian property of the unknown species or OTUs (operational taxonomic units).

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

MBBC

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Java

:: DOWNLOAD

 MBBC

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2015 Feb 5;16(1):36. [Epub ahead of print]
MBBC: an efficient approach for metagenomic binning based on clustering.
Wang Y, Hu H, Li X.

SIOMICS 3.0 – Systematic Identification Of Motifs In ChIP-Seq data

SIOMICS 3.0

:: DESCRIPTION

SIOMICS is a software developed to de novo identify motifs in large sequence datasets such as those from ChIP-seq experiments. The output of the software is the ranked motifs and motif modules (significantly co-occurring motif combinations). The statistical evaluation of the predicted motifs and motif modules is also provided.

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

SIOMICS

:: REQUIREMENTS

  • Linux/ Windows
  • Python
  • Tkinter
  • Java

:: DOWNLOAD

 SIOMICS

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2014 Mar;42(5):e35. doi: 10.1093/nar/gkt1288. Epub 2013 Dec 9.
SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data.
Ding J, Hu H, Li X.

TreeGibbsSampler – Identifying Conserved Motifs without Aligning Orthologous Sequences

TreeGibbsSampler

:: DESCRIPTION

Tree Gibbs Sampler is a software for identifying motifs by simultaneously using the motif overrepresentation property and the motif evolutionary conservation property. It identifies motifs without depending on pre-aligned orthologous sequences, which makes it useful for the extraction of regulatory elements in multiple genomes of both closely related and distant species.

::DEVELOPER

Xiaohui Cai, Haiyan Nancy Hu ,Xiaoman Shawn Li

:: SCREENSHOTS

TreeGibbsSampler

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 Tree Gibbs Sampler

:: MORE INFORMATION

Citation:

Bioinformatics. 2007 Aug 1;23(15):2013-4. Epub 2007 May 31.
Tree Gibbs Sampler: identifying conserved motifs without aligning orthologous sequences.
Cai X, Hu H, Li XS.

MOPAT – Predict recurrent Cis-regulatory Modules from known Motif

MOPAT

:: DESCRIPTION

MOPAT (Motif Pair Tree) identifies CRMs through the identification of motif modules, groups of motifs co-ccurring in multiple CRMs. It can identify orthologous CRMs without multiple alignments. It can also find CRMs given a large number of known motifs.

::DEVELOPER

Data Integration and Knowledge Discovery Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 MOPAT

:: MORE INFORMATION

Citation:

Hu J, Hu H, Li X.
MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs.
Nucleic Acids Res. 2008; 36(13):4488-97

MERCED 1.1 – Systematic Discovery of Cis-regulatory Elements in C.reinhardtii

MERCED 1.1

:: DESCRIPTION

MERCED (modeling evolution rate across species for cis-regulatory element discovery) is a server about systematic discovery of cis-regulatory elements in C.reinhardtii.

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MERCED

:: MORE INFORMATION

Citation:

Plant Physiol. 2012 Oct;160(2):613-23. doi: 10.1104/pp.112.200840. Epub 2012 Aug 22.
Systematic prediction of cis-regulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics.
Ding J, Li X, Hu H.

CCAT 3.0 – Control based ChIPSeq Analysis Tools

CCAT 3.0

:: DESCRIPTION

CCAT is a software package for the analysis of ChIP-seq data with negative control.

:: DEVELOPER

Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 CCAT

:: MORE INFORMATION

Citation

A signal-noise model for significance analysis of ChIP-seq with negative control.
Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK.
Bioinformatics. 2010 May 1;26(9):1199-204

BatMeth 1.04b – Improved Mapper for Bisulfite Sequencing Reads on DNA Methylation

BatMeth 1.04b

:: DESCRIPTION

BatMeth is an algorithm that integrates novel mismatch counting, list filtering, mismatch stage filtering and fast mapping onto two indexes to improve unique mapping rate, speed and precision.

::DEVELOPER

Sung Wing Kin, Ken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BatMeth

:: MORE INFORMATION

Citation

Genome Biol. 2012 Oct 3;13(10):R82. [Epub ahead of print]
BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation.
Lim JQ, Tennakoon C, Li G, Wong E, Ruan Y, Wei CL, Sung WK.