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.

MatAlign V4A – Comparison, Alignment of PSSMs

MatAlign V4A

:: DESCRIPTION

MatAlign (Matrix Aligner) allows comparison among many matrices.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MatAlign

:: MORE INFORMATION

HHblits 3.2.0 – Homology Detection by Iterative HMM-HMM Comparison

HHblits 3.2.0

:: DESCRIPTION

HHblits is the first iterative method based on the pairwise comparison of profile Hidden Markov Models. In benchmarks it achieves better runtimes than other iterative sequence search methods such as PSI-BLAST or HMMER3 by using a fast prefilter based on profile-profile comparison. Furthermore, HHblits greatly improves upon PSI-BLAST and HMMER3 in terms of sensitivity/selectivity and alignment quality.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

  Part of HH-suite

:: MORE INFORMATION

Citation

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
Remmert M, Biegert A, Hauser A, Söding J.
Nat Methods. 2011 Dec 25;9(2):173-5. doi: 10.1038/nmeth.1818.

Vienna RNA Package 2.4.14 – RNA Secondary Structure Prediction & Comparison

Vienna RNA Package 2.4.14

:: DESCRIPTION

Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

Vienna RNA WebServers

::DEVELOPER

Theoretical Biochemistry Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Mac OsX/ Windows

:: DOWNLOAD

Vienna RNA

:: MORE INFORMATION

Citation

Methods Mol Biol. 2015;1269:307-26. doi: 10.1007/978-1-4939-2291-8_19.
The ViennaRNA web services.
Gruber AR1, Bernhart SH, Lorenz R.

Ivo L. Hofacker
Vienna RNA secondary structure serverNucl.
Acids Res. (2003) 31 (13): 3429-3431

Lorenz, Ronny and Bernhart, Stephan H. and Höner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L.
ViennaRNA Package 2.0
Algorithms for Molecular Biology, 6:1 26, 2011, doi:10.1186/1748-7188-6-26

Survcomp 1.34.0 – Performance Assessment and Comparison for Survival Analysis

Survcomp 1.34.0

:: DESCRIPTION

Survcomp is an R package providing functions to assess and to compare the performance of risk prediction (survival) models.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R/Bioconductor

:: DOWNLOAD

 Survcomp

:: MORE INFORMATION

Citation:

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models.
Schröder MS, Culhane AC, Quackenbush J, Haibe-Kains B.
Bioinformatics. 2011 Nov 15;27(22):3206-8. doi: 10.1093/bioinformatics/btr511.

dali_sp – Script for DaliLite to perform Serial Structure Comparison

dali_sp

:: DESCRIPTION

dali_sp is a wrapper script for DaliLite to perform serial structure comparison and to merge output pairwise alignments into single multiple alignment.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 dali_sp

:: MORE INFORMATION

LayerCake 20150814 – Visual Comparison of Viral Deep Sequencing data

LayerCake 20150814

:: 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.

ProPhylo 1.02 – Phylogenetic Profile comparison program using Partial Phylogenetic Profile algorithm

ProPhylo 1.02

:: DESCRIPTION

ProPhylo is a high-performance parallel software to run phylogenetic profile searches at genome-scale.

::DEVELOPER

Malay K Basu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  ProPhylo

:: MORE INFORMATION

Citation

Basu, M. K., Selengut, J. D., Haft, D. H.
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process
BMC Bioinformatics. 2011 Dec 01; 12: 434.

SMAP 2.0 – Software for Ligand Binding Site Comparison

SMAP 2.0

:: DESCRIPTION

SMAP software package is designed for the comparison and the similarity search of protein three-dimensional motifs independent on the sequence order.

::DEVELOPER

Lei Xie

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Perl

:: DOWNLOAD

 SMAP

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W441-4. doi: 10.1093/nar/gkq400. Epub 2010 May 19.
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison.
Ren J1, Xie L, Li WW, Bourne PE.

ClusCo 0.3 – Clustering and Comparison of Protein Models

ClusCo 0.3

:: DESCRIPTION

ClusCo is a software for GPU/CPU clustering and comparison of protein models.

::DEVELOPER

Laboratory of Theory of Biopolymers,  University of Warsaw

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ClusCo

:: MORE INFORMATION

Citation

ClusCo: clustering and comparison of protein models.
Jamroz M, Kolinski A.
BMC Bioinformatics. 2013 Feb 22;14:62. doi: 10.1186/1471-2105-14-62.