STON – Protein 3D Structure Comparison

STON

:: DESCRIPTION

STON is a new algorithm to find aligned residues in two proteins with desired rmsd value.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Comput Biol Med. 2009 Feb;39(2):166-72. doi: 10.1016/j.compbiomed.2008.12.004. Epub 2009 Jan 23.
STON: A novel method for protein three-dimensional structure comparison.
Eslahchi C1, Pezeshk H, Sadeghi M, Massoud Rahimi A, Maboudi Afkham H, Arab S.

RRS – Comparison of regulatory DNA Sequences

RRS

:: DESCRIPTION

RRS (Regulatory Region Scoring)  is a new computational framework for the detection of functional conservation of regulatory sequences using predicted occupancy levels of transcription factors of interest.

::DEVELOPER

Dr Sascha Ott

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • C /R

:: DOWNLOAD

 RRS

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Oct 1;26(19):2391-7. doi: 10.1093/bioinformatics/btq453. Epub 2010 Aug 9.
An alignment-free model for comparison of regulatory sequences.
Koohy H1, Dyer NP, Reid JE, Koentges G, Ott S.

NCT 1.1.0 – The Network Comparison Toolkit

NCT 1.1.0

:: DESCRIPTION

NCT is a Java library developed to allow the comparison of biological networks. The software was developed to be modular and easily extended.

::DEVELOPER

the Ideker Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NCT

:: MORE INFORMATION

CEpBrowser 20150219 – Comparison of Epigenomic Modifications across Species

CEpBrowser 20150219

:: DESCRIPTION

CEpBrowser (Comparative Epigenome Browser) is a gene-centric genome browser that visualize the genomic features of multiple species with color-coded orthologous regions, aiding users in comparative genomic research. The genome browser is adapted from UCSC Genome Browser and the orthologous regions are generated from cross-species lift-over pairs.

::DEVELOPER

Zhong Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 1;29(9):1223-5. doi: 10.1093/bioinformatics/btt114. Epub 2013 Mar 29.
Enabling interspecies epigenomic comparison with CEpBrowser.
Cao X, Zhong S.

D2Z 0.1 – Alignment Free Comparison of Regulatory Sequences

D2Z 0.1

:: DESCRIPTION

D2Z is based on comparing the frequencies of all fixed-length words in the two sequences. An important, novel feature of the score is that it is comparable across sequence pairs drawn from arbitrary background distributions.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

D2Z Source Code

:: MORE INFORMATION

Citation:

A statistical method for alignment-free comparison of regulatory sequences
Miriam R. Kantorovitz,Gene E. Robinson, Saurabh Sinha.
Bioinformatics. 2007 Jul 1;23(13):i249-55.

MaxCluster – Protein Structure Comparison and Clustering

MaxCluster

:: DESCRIPTION

MaxCluster (MaxSub and Clustering) is a command-line tool for the comparison of protein structures. It provides a simple interface for a large number of common structure comparison tasks. A key feature of the program is the ability to process thousands of structures, either against a single reference protein or in an all-verses-all comparison.
::DEVELOPER

Alex Herbert , Structural Bioinformatics Group, Imperial College

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • GCC

:: DOWNLOAD

 MaxCluster

:: MORE INFORMATION

LayerCake 20171023 – Visual Comparison of Viral Deep Sequencing data

LayerCake 20171023

:: DESCRIPTION

LayerCake is a tool created for visualizing viral variation from next generation sequencing data

::DEVELOPER

collaboration between labs associated with UW Computer Sciences andUW Pathology & Laboratory Medicine Departments.

:: SCREENSHOTS

LayerCake

:: REQUIREMENTS

  • Windows / MacOsX
  • Java

:: DOWNLOAD

 LayerCake

:: MORE INFORMATION

Citation

LayerCake: a tool for the visual comparison of viral deep sequencing data.
Correll M, Bailey AL, Sarikaya A, O’Connor DH, Gleicher M.
Bioinformatics. 2015 Jul 7. pii: btv407.

tRanslatome 1.24.0 – Comparison between multiple levels of Gene Expression

tRanslatome 1.24.0

:: DESCRIPTION

tRanslatome is a R/Bioconductor package, which is a complete platform for the simultaneous pairwise analysis of transcriptome, translatome and proteome data.

::DEVELOPER

Laboratory of Translational Genomics , CIBIO

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R/Bioconductor

:: DOWNLOAD

 tRanslatome

:: MORE INFORMATION

Citation

tRanslatome: an R/Bioconductor package to portray translational control.
Tebaldi T, Dassi E, Kostoska G, Viero G, Quattrone A.
Bioinformatics. 2014 Jan 15;30(2):289-91. doi: 10.1093/bioinformatics/btt634.

RadCon 1.1.6 – Phylogenetic Tree Consensus & Comparison Program

RadCon 1.1.6

:: DESCRIPTION

RadCon is a phylogenetic tree consensus and comparison program for Macs (OS 7.5 – 9).Implemented methods include the strict reduced consensus method, leaf stability, cladistic information content, double decay analysis and matrix representation with parsimony.

::DEVELOPER

RadCon team

:: SCREENSHOTS

:: REQUIREMENTS

  • Mac(OS 7.5 – 9)

:: DOWNLOAD

 RadCon

:: MORE INFORMATION

Citation

Joseph L. Thorley and Roderic D. M. Page
RadCon: phylogenetic tree comparison and consensus
Bioinformatics (2000) 16 (5): 486-487.

ChIPseeker 1.22.0 – ChIP peak Annotation, Comparison & Visualization

ChIPseeker 1.22.0

:: DESCRIPTION

ChIPseeker is an R package for annotating ChIP-seq data analysis.

::DEVELOPER

Guangchuang YU,

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux/MacOsX
  • R
  • Bioconductor

:: DOWNLOAD

 ChIPseeker

:: MORE INFORMATION

Citation:

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.
Yu G, Wang LG, He QY.
Bioinformatics. 2015 Mar 11. pii: btv145.