BEDTools 2.29.0 – Compare Genomic Features

BEDTools 2.29.0

:: 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: BEDGFF/GTFVCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by “streaming” several BEDTools together.

::DEVELOPER

The Quinlan Lab , Ira Hall 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.

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

TreeMap 3.0b – Compare Host & Parasite Trees

TreeMap 3.0b

:: DESCRIPTION

TreeMap is an experimental program for comparing host and parasite trees. TREEMAP performs cophylogeny mapping from a dependent evolutionary tree (e.g., a group of parasites) into an independent one (e.g., the hosts of those parasites), in order to recover the best possible coevolutionary explanation for the relationship between the two . The archetypal example is of the coevolution of pocket gophers and their chewing lice.

::DEVELOPER

Dr. Michael Charleston

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

TreeMap

:: MORE INFORMATION

Citation

M. A. Charleston and D. L. Robertson.
Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny.
Syst Biol, 51(3):528-535, Jun 2002.

MirCompare – Algorithm to Compare Plant and Mammalian miRNAs

MirCompare

:: 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

  NO

:: 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.

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

CompNet

:: 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

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

 NO

:: 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

COSER – Compare Genomes with Segmental Duplications and Rearrangements

COSER

:: DESCRIPTION

COSER is a software to COmpare genomes with SEgmental duplications and Rearrangement

::DEVELOPER

Laboratory for Computational Biology and Bioinformatics (LCBB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 COSER

:: MORE INFORMATION

Citation

Comparing genomes with rearrangements and segmental duplications.
Shao M, Moret BM.
Bioinformatics. 2015 Jun 15;31(12):i329-i338. doi: 10.1093/bioinformatics/btv229.

EC-BLAST – A Novel Tool to Map Reactions and Compare Enzymes

EC-BLAST

:: DESCRIPTION

EC-BLAST is an algorithm and Web tool for quantitative similarity searches between enzyme reactions at three levels: bond change, reaction center and reaction structure similarity.

::DEVELOPER

Thornton group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

EC-BLAST: a tool to automatically search and compare enzyme reactions.
Rahman SA, Cuesta SM, Furnham N, Holliday GL, Thornton JM.
Nat Methods. 2014 Feb;11(2):171-4. doi: 10.1038/nmeth.2803.

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

:: 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