APPLES 20120911 – Analyse Promoter Sequences on a Genome-wide scale

APPLES 20120911

:: DESCRIPTION

The APPLES (Analysis of Plant Promoter-Linked Elements) software package is a set of tools to analyse promoter sequences on a genome-wide scale.

::DEVELOPER

Dr Sascha Ott

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/virtual machine

:: DOWNLOAD

 APPLES

:: MORE INFORMATION

GeneSyn 1.1 – Detect Conserved Gene Order across Genomes

GeneSyn 1.1

:: DESCRIPTION

GeneSyn is a software for the detection of highly conserved gene arrangements through the analysis of multiple gene orders in different genomes.

::DEVELOPER

Giulio Pavesi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GeneSyn

:: MORE INFORMATION

Citation:

GeneSyn: a tool for detecting conserved gene order across genomes.
Pavesi G, Mauri G, Iannelli F, Gissi C, Pesole G.
Bioinformatics. 2004 Jun 12;20(9):1472-4. Epub 2004 Feb 19.

FunSeq2 2.1.6 – Prioritize Regulatory Mutations from Cancer Genome Sequencing

FunSeq2 2.1.6

:: DESCRIPTION

FunSeq2 is specialized to prioritize somatic variants from cancer whole genome sequencing.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

FunSeq2

:: MORE INFORMATION

Citation:

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.
Fu Y, Liu Z, Lou S, Bedford J, Mu XJ, Yip KY, Khurana E, Gerstein M.
Genome Biol. 2014;15(10):480.

APEG – Affinity Prediction by Epigenome and Genome

APEG

:: DESCRIPTION

APEG uses a biophysical model to analyze transcription (TF)-DNA binding data, such as ChIP-seq data by incorporating epigenomic modifications and genome sequence data. This model can learn synergistic and antagonistic interactions between specific TFs and epigenomic modifications from genome-wide TF binding and epigenomic data.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

APEG

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2013;9(12):e1003367. doi: 10.1371/journal.pcbi.1003367.
Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions.
Chen CC, Xiao S, Xie D, Cao X, Song CX, Wang T, He C, Zhong S.

SCRMshaw – Genome-wide Supervised CRM Prediction

SCRMshaw

:: DESCRIPTION

SCRMshaw is a genome-wide CRM prediction program that learns parameters from a list of CRMs that regulates the same spatial/temporal gene expression pattern, and predicts CRMs with similar functionality genome-wide. The SCRMshaw program is designed for predicting CRMs in the genome sequence of model/non-model species given the known CRMs provided by users. Users can also choose three different scoring schemes to predict CRMs: IMM, PAC and HexMCD.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SCRMshaw

:: MORE INFORMATION

Citation:

Dev Biol. 2016 Aug 15;416(2):402-13. doi: 10.1016/j.ydbio.2016.06.031.
Redeployment of a conserved gene regulatory network during Aedes aegypti development.
Suryamohan K, Hanson C, Andrews E, Sinha S, Scheel MD, Halfon MS.

Weaver – Allele-Specific Quantification of Structural Variations in Cancer Genomes

Weaver

:: DESCRIPTION

Weaver quantifies allele-specific copy number alteration and allele-specific structural variation in cancer genome using whole-genome sequencing reads.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Weaver

:: MORE INFORMATION

Citation

Allele-Specific Quantification of Structural Variations in Cancer Genomes.
Li Y, Zhou S, Schwartz DC, Ma J.
Cell Syst. 2016 Jul;3(1):21-34. doi: 10.1016/j.cels.2016.05.007.

Phylo-HMRF – Comparing 3D Genome Organization in Multiple Species

Phylo-HMRF

:: DESCRIPTION

Phylo-HMRF (Phylogenetic Hidden Markov Random Field model) identifies evolutionary patterns of 3D genome based on multi-species Hi-C data.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

Phylo-HMRF

:: MORE INFORMATION

Citation

Cell Syst. 2019 Jun 26;8(6):494-505.e14. doi: 10.1016/j.cels.
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.
Yang Y, Zhang Y, Ren B, Dixon JR, Ma J.

MetaBAT 2.12.1 – Reconstructing Single Genomes from Complex Microbial Communities

MetaBAT 2.12.1

:: DESCRIPTION

MetaBAT is an efficient tool for accurately reconstructing single genomes from complex microbial communities.

::DEVELOPER

Zhong Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • C++ Compiler

:: DOWNLOAD

 MetaBAT

:: MORE INFORMATION

Citation

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.
Kang DD, Froula J, Egan R, Wang Z.
PeerJ. 2015 Aug 27;3:e1165. doi: 10.7717/peerj.1165.

CoMoFinder – Identify Composite Network Motifs in Genome-scale Co-regulatory Networks

CoMoFinder

:: DESCRIPTION

CoMoFinder strives to discover reliable composite network motifs in co-regulatory networks which consist of microRNAs, transcriptional regulators and genes.

::DEVELOPER

Yue Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • JDK

:: DOWNLOAD

 CoMoFinder

:: MORE INFORMATION

Citation:

A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human.
Liang C, Li Y, Luo J, Zhang Z.
Bioinformatics. 2015 Mar 18. pii: btv159

xMAN 20060925 – MAp OligoNucleotides to Subject Genome

xMAN 20060925

:: DESCRIPTION

xMAN (extreme MApping of OligoNucleotides) is a simple and efficient method for the mapping of millions of query oligonucleotide fragments to the subject genome of any given length. xMAN is at least an order of magnitude faster than other popular existing tools.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  xMAN

:: MORE INFORMATION

Citation:

Li W, Carroll JS, Brown M, Liu S.
xMAN: extreme MApping of OligoNucleotides.
BMC Genomics. 2008;9 Suppl 1:S20.