ProtRe-CN – Protein Remote Homology Detection

ProtRe-CN

:: DESCRIPTION

ProtRe-CN is a novel ranking method for protein remote homology detection by combining classification methods and network methods via Learning to Rank.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ProtRe-CN

:: MORE INFORMATION

Citation

Shao J, Chen J, Liu B.
ProtRe-CN: Protein Remote Homology Detection by Combining Classification Methods and Network Methods via Learning to Rank.
IEEE/ACM Trans Comput Biol Bioinform. 2021 Aug 30;PP. doi: 10.1109/TCBB.2021.3108168. Epub ahead of print. PMID: 34460380.

MotifSuite 201401 – Probabilistic Motif Detection

MotifSuite 201401

:: DESCRIPTION

MotifSuite is a software for probabilistic motif detection. Probabilistic motif detection requires a multi-step approach going from the actual de novo regulatory motif finding up to a tedious assessment of the predicted motifs. MotifSuite, a user-friendly web interface streamlines this analysis flow. Its core consists of two post-processing procedures that allow prioritizing the motif detection output. The tools offered by MotifSuite are built around the well-established motif detection tool MotifSampler and can also be used in combination with any other probabilistic motif detection tool.

::DEVELOPER

 Prof. Dr. Kathleen Marchal 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MotifSuite

:: MORE INFORMATION

Citation:

M. Claeys; V. Storms; H. Sun; T. Michoel; K. Marchal.
MotifSuite: workflow for probabilistic motif detection and assessment.
Bioinformatics 2012; doi: 10.1093/bioinformatics/bts293

ModuleDigger – An Itemset Mining framework for the Detection of Cis-regulatory Modules

ModuleDigger

:: DESCRIPTION

ModuleDigger is an itemset mining based strategy for computationally detecting cis-regulatory modules (CRMs) in a set of genes.

::DEVELOPER

 Kathleen Marchal 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ModuleDigger

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S30.
ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules.
Sun H, De Bie T, Storms V, Fu Q, Dhollander T, Lemmens K, Verstuyf A, De Moor B, Marchal K.

Varclus – Detection of Positive Selection in Genes and Genomes through Variation Clusters

Varclus

:: DESCRIPTION

Varclus is a perl utility to identify clusters of amino acid or nucleotide changes in a sequence that are too tightly spaced to have occurred by chance alone.

::DEVELOPER

Andreas Wagner Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

 Varclus

:: MORE INFORMATION

Citation:

Wagner, A. (2007)
Rapid detection of positive selection in genes and genomes through variation clusters.
Genetics 176: 2451–2463

SEGtool 1.3 – Specifically Expressed Gene Detection

SEGtool 1.3

:: DESCRIPTION

SEGtool is an R package with self-adaptive function and high accuracy for specifically expressed gene (SEG, also known as tissue specific gene) detection.

::DEVELOPER

An-Yuan Guo’s Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

SEGtool

:: MORE INFORMATION

Citation

Zhang Q, Liu W, Liu C, Lin SY, Guo AY.
SEGtool: a specifically expressed gene detection tool and applications in human tissue and single-cell sequencing data.
Brief Bioinform. 2018 Nov 27;19(6):1325-1336. doi: 10.1093/bib/bbx074. PMID: 28981576.

SvABA 1.1.0 – Structural Variation and Indel Detection by local Assembly

SvABA 1.1.0

:: DESCRIPTION

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly.

::DEVELOPER

Jeremiah Wala (jwala@broadinstitute.org) — Rameen Berkoukhim lab — Dana Farber Cancer Institute, Boston, MA.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SvABA

:: MORE INFORMATION

Citation

Wala JA, Bandopadhayay P, Greenwald NF, O’Rourke R, Sharpe T, Stewart C, Schumacher S, Li Y, Weischenfeldt J, Yao X, Nusbaum C, Campbell P, Getz G, Meyerson M, Zhang CZ, Imielinski M, Beroukhim R.
SvABA: genome-wide detection of structural variants and indels by local assembly.
Genome Res. 2018 Apr;28(4):581-591. doi: 10.1101/gr.221028.117. Epub 2018 Mar 13. PMID: 29535149; PMCID: PMC5880247.

MSPocket 1.1 – Detection and Graphical Analysis of Protein Surface Pockets

MSPocket 1.1

:: DESCRIPTION

MSPocket is an orientation independent program for the detection and graphical analysis of protein surface pockets.

::DEVELOPER

Zhu, Hongbo.

:: SCREENSHOTS

MSPocket

:: REQUIREMENTS

  • Linux / Windows /Mac OsX
  • Python
  • Biopython
  • MSMS
  • PyMOL

:: DOWNLOAD

 MSPocket

:: MORE INFORMATION

Citation

Zhu H, Pisabarro MT.
MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets.
Bioinformatics. 2011 Feb 1;27(3):351-8.

ORCAtk 1.0.0 – Transcription Factor Binding Site Detection using Phylogenetic Footprinting

ORCAtk 1.0.0

:: DESCRIPTION

The ORCA Toolkit is a system for finding putative regulatory regions and transcription factor binding sites (TFBSs) within those regions.

::DEVELOPER

The Wasserman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Perl

:: DOWNLOAD

 ORCAtk

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jan;37(Database issue):D54-60. doi: 10.1093/nar/gkn783. Epub 2008 Oct 29.
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences.
Portales-Casamar E, Arenillas D, Lim J, Swanson MI, Jiang S, McCallum A, Kirov S, Wasserman WW.

ClineHelpR v1.1 – Genomic Cline Outlier Detection and Visualization

ClineHelpR v1.1

:: DESCRIPTION

ClineHelpR is an R-package for visualizing genomic clines and detecting outlier loci using output generated by two popular software packages, bgc and Introgress

::DEVELOPER

Bradley Martin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R

:: DOWNLOAD

ClineHelpR

:: MORE INFORMATION

Citation

Martin BT, Chafin TK, Douglas MR, Douglas ME.
ClineHelpR: an R package for genomic cline outlier detection and visualization.
BMC Bioinformatics. 2021 Oct 16;22(1):501. doi: 10.1186/s12859-021-04423-x. PMID: 34656096; PMCID: PMC8520269.

HiNT v2.2.7 – Hi-C for Copy Number Variation and Translocation Detection

HiNT v2.2.7

:: DESCRIPTION

HiNT is a computational method to detect CNVs and Translocations from Hi-C data.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Perl
  • R package
  • Python

:: DOWNLOAD

HiNT

:: MORE INFORMATION

Citation

Wang S, Lee S, Chu C, Jain D, Kerpedjiev P, Nelson GM, Walsh JM, Alver BH, Park PJ.
HiNT: a computational method for detecting copy number variations and translocations from Hi-C data.
Genome Biol. 2020 Mar 23;21(1):73. doi: 10.1186/s13059-020-01986-5. PMID: 32293513; PMCID: PMC7087379.