MatCompare 1.3 – Compare Transcription Factor Binding Site (TFBS) position Frequency Matrices (PFMs)

MatCompare 1.3

:: DESCRIPTION

The MatCompare software provides methods for comparing transcription factor binding site (TFBS) position frequency matrices (PFMs). The user has a choice of using the Kullback-Leibler divergence, the chi squared test or the Fisher-Irwin exact test of similarity.

::DEVELOPER

Michael Zhang Computational Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

MatCompare

:: MORE INFORMATION

Citation:

Dustin E Schones, Pavel Sumazin and Michael Q Zhang
Similarity of position frequency matrices for transcription factor binding sites
Bioinformatics 2005 21(3):307-313; doi:10.1093/bioinformatics/bth480

Censor 4.2.29 – Compares and Masks Protein or Nucleotide Sequences

Censor 4.2.29

:: DESCRIPTION

CENSOR is a software tool which screens query sequences against a reference collection of repeats and “censors” (masks) homologous portions with masking symbols, as well as generating a report classifying all found repeats.

:: DEVELOPER

Genetic Information Research Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ compiler
NCBI BLAST

:: DOWNLOAD

Censor

:: MORE INFORMATION

Citation:

Kohany O, Gentles AJ, Hankus L, Jurka J
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.
BMC Bioinformatics, 2006 Oct 25;7:474

BEDTools 2.30.0 – Compare Genomic Features

BEDTools 2.30.0

:: DESCRIPTION

The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by “streaming” several BEDTools together.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

BEDTools

:: MORE INFORMATION

Citation:

Quinlan AR and Hall IM, 2010.
BEDTools: a flexible suite of utilities for comparing genomic features.
Bioinformatics. 26, 6, pp. 841–842.

PocketMatch 2.1 – Compare a pair of Binding Sites

PocketMatch 2.1

:: DESCRIPTION

PocketMatch is a software for comparison of binding sites in a frame invariant manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites.

::DEVELOPER

Chandra lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PocketMatch

:: MORE INFORMATION

Citation

Kalidas Yeturu and Nagasuma Chandra(2008)
PocketMatch: A new algorithm to compare binding sites in protein structures
BMC Bioinformatics 2008, 9:543

CompNet – A GUI based tool to Compare Multiple Biological Interaction Networks

CompNet

:: DESCRIPTION

CompNet, a GUI based network comparison tool , allows to visually compare multiple networks based on node and edge similarities.

::DEVELOPER

CompNet team

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows
R package

:: DOWNLOAD

CompNet

:: MORE INFORMATION

Citation:

CompNet: a GUI based tool for comparison of multiple biological interaction networks.
Kuntal BK, Dutta A, Mande SS.
BMC Bioinformatics. 2016 Apr 26;17(1):185. doi: 10.1186/s12859-016-1013-x

MirCompare 2.0 – Algorithm to Compare Plant and Mammalian miRNAs

MirCompare 2.0

:: DESCRIPTION

MirCompare is an innovative algorithm developed to compare sets of microRNAs belonging to different kingdoms, for their capacity to bind host mRNAs.

::DEVELOPER

MirCompare team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Bioinformatics Prediction and Experimental Validation of MicroRNAs Involved in Cross-Kingdom Interaction.
Pirrò S, Minutolo A, Galgani A, Potestà M, Colizzi V, Montesano C.
J Comput Biol. 2016 Jul 18.

Gardenia – Compare & Align RNA Structures

Gardenia

:: DESCRIPTION

Gardenia is a program that Compares & aligns RNA secondary structures,without pseudoknots. The resulting alignment takes into account both the primary structure and the secondary structure.

::DEVELOPER

Bonsai Bioinformatics – INRIA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
C Complier

:: DOWNLOAD

Gardenia

:: MORE INFORMATION

Citation

Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Helene Touzet
Alignment of RNA structures
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008

TreeKO – Compare Phylogenetic Trees

TreeKO

:: DESCRIPTION

TreeKO is a python package used to compare phylogenetic trees

::DEVELOPER

Bioinformatics and Genomics @ CRG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX/ Windows
Python

:: DOWNLOAD

TreeKO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 May;39(10):e66. doi: 10.1093/nar/gkr087. Epub 2011 Feb 18.
TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees.
Marcet-Houben M, Gabaldón T.

jpHMM 201503 – Compare a Sequence to a Multiple Alignment of a Sequence Family

jpHMM 201503

:: DESCRIPTION

jpHMM (jumping profile Hidden Markov Model) is a probabilistic approach to compare a sequence to a multiple alignment of a sequence family. The jpHMM web server at GOBICS is a tool for the detection of genomic recombinations in HIV-1 and HBV.

jpHMM Online Version

::DEVELOPER

the Department of Bioinformatics of the University of Göttingen and the Los Alamos HIV Sequence Database Group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

jpHMM

:: MORE INFORMATION

Citation

A.-K. Schultz, M. Zhang, T. Leitner, C. Kuiken, B. Korber, B. Morgenstern, M. Stanke.
A Jumping Profile Hidden Markov Model and Applications to Recombination Sites in HIV and HCV Genomes.
BMC Bioinformatics 7:265. 2006

comPARE – PARE Validated miRNA Targets

comPARE

:: DESCRIPTION

comPARE is a web resource for plant miRNA target analysis.

::DEVELOPER

the Meyers lab at the University of Delaware.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Oct;42(18):e139. doi: 10.1093/nar/gku693. Epub 2014 Aug 12.
sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software.
Kakrana A, Hammond R, Patel P, Nakano M, Meyers BC