ShortStack 3.8.5 – Comprehensive Annotation and Quantification of small RNA genes

:: DESCRIPTION

ShortStack is a tool developed to process and analyze smallRNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes.

::DEVELOPER

Axtell Lab @ Penn State

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ShortStack

:: MORE INFORMATION

Citation:

Axtell MJ.
ShortStack: comprehensive annotation and quantification of small RNA genes.
RNA. 2013 Jun;19(6):740-51. doi: 10.1261/rna.035279.112. Epub 2013 Apr 22. PMID: 23610128; PMCID: PMC3683909.

SPPS – Sequence-based Protein Partners Search

:: DESCRIPTION

SPPS is an open-accessed web server for rapidly exploring potential partners of proteins, by searching over a large repertoire of proteins across many species. SPPS provides a database containing more than 60,000 protein sequences with annotations and a SVM based protein-partner search engine.

::DEVELOPER

Molecular Design Labrotary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2012;7(1):e30938. doi: 10.1371/journal.pone.0030938. Epub 2012 Jan 26.
SPPS: a sequence-based method for predicting probability of protein-protein interaction partners.
Liu X1, Liu B, Huang Z, Shi T, Chen Y, Zhang J.

RINalyzer 2.0 – Cytoscape plugin of Visualization and Analysis of Biomolecular Networks

:: DESCRIPTION

RINalyzer is a Java plugin for Cytoscape, a free open-source software platform for visualization and analysis of biomolecular networks. This plugin allows the simultaneous visualization and interactive analysis of residue interaction networks (RINs) together with the corresponding 3D protein structures displayed in UCSF Chimera. It also provides a comprehensive set of topological centrality measures to gain additional insights into the structural and functional role of interacting residues.

::DEVELOPER

RINalyzer team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 RINalyzer

:: MORE INFORMATION

Citation:

Doncheva, N.T., Klein, K., Domingues, F.S., Albrecht, M. (2011):
Analyzing and visualizing residue networks of protein structures.
Trends in Biochemical Sciences, 36(4): 179-182.

SProtP – Recognition of Short-lived Human Proteins

:: DESCRIPTION

SProtP is a web server of recognition of short-lived proteins based on sequence-derived features in human cells

::DEVELOPER

Oribel PortaPlay Stools, Multi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2011;6(11):e27836. doi: 10.1371/journal.pone.0027836. Epub 2011 Nov 16.
SProtP: a web server to recognize those short-lived proteins based on sequence-derived features in human cells.
Song X1, Zhou T, Jia H, Guo X, Zhang X, Han P, Sha J.

FISH Finder 0.27 – A High-Throughput Tool for Analyzing FISH Images

:: DESCRIPTION

Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus.FISH Finder is a graphical software tool to automatically analyze FISH images that vary significantly.

::DEVELOPER

The Imaging Sciences Lab @ FSU

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 FISH Finder

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Apr 1;27(7):933-8. doi: 10.1093/bioinformatics/btr053. Epub 2011 Feb 9.
FISH Finder: a high-throughput tool for analyzing FISH images.
Shirley JW1, Ty S, Takebayashi S, Liu X, Gilbert DM.

ERDS 1.1 – Calling CNVs from Whole Genome NGS data

:: DESCRIPTION

ERDS (estimation by read depth with single-nucleotide variants) is designed for detection of copy number variants (CNVs) on human genomes from next generation sequence data, utilizing information from read depth of short reads and SNV heterozygosity.

::DEVELOPER

Mingfu Zhu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ERDS

:: MORE INFORMATION

Citation

Am J Hum Genet. 2012 Sep 7;91(3):408-21. doi: 10.1016/j.ajhg.2012.07.004. Epub 2012 Aug 30.
Using ERDS to infer copy-number variants in high-coverage genomes.
Zhu M1, Need AC, Han Y, Ge D, Maia JM, Zhu Q, Heinzen EL, Cirulli ET, Pelak K, He M, Ruzzo EK, Gumbs C, Singh A, Feng S, Shianna KV, Goldstein DB.

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GEsnpx 1.1 / GEsnpxPara 1.3 – Genetic Ensemble approach for Gene-gene Interaction Identification

:: DESCRIPTION

GEsnpx is a Java implementation of genetic ensemble algorithm for gene-gene interaction identification

GEsnpxPara is a parallel version of genetic ensemble algorithm

::DEVELOPER

GEsnpx team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

 GEsnpx / GEsnpxPara

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Oct 21;11:524. doi: 10.1186/1471-2105-11-524.
A genetic ensemble approach for gene-gene interaction identification.
Yang P1, Ho JW, Zomaya AY, Zhou BB.

HiCat – Hi-C data analysis tool

:: DESCRIPTION

HiCat is an Hi-C data analysis tool. Importantly, HiCat is focussed on analysis of larger structural features of chromosomes and on comparative studies.

::DEVELOPER

Ueli Grossniklaus’s group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX

:: DOWNLOAD

 HiCat

:: MORE INFORMATION

Citation

Grob S, Schmid MW, Grossniklaus U. (2014)
HiC Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila.
Molecular Cell, 55(5): 678-693

TuRF-E 1.0 – Gene-gene Interaction Giltering with Ensemble of Filters

:: DESCRIPTION

Providing TuRF-E program for SNP interaction filtering.

::DEVELOPER

TuRF-E team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Perl
:: DOWNLOAD

 TuRF-E

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S10. doi: 10.1186/1471-2105-12-S1-S10.
Gene-gene interaction filtering with ensemble of filters.
Yang P1, Ho JW, Yang YH, Zhou BB.

Rcount – Simple and Flexible RNA-Seq Read Counting

:: DESCRIPTION

Portland Timbers Army Scarf is a software for simple and flexible RNA-Seq read counting. Rcount allows the user to assign priorities to certain feature types (e.g. higher priority for protein-coding genes compared to rRNA- coding genes) or to add flanking regions.

::DEVELOPER

LEICA MOK-93 ( 10445111 ) PAIR OF 10X / 21B MICROSCOPE EYEPIECES

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX

:: DOWNLOAD

 Rcount

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 15. pii: btu680.
Rcount: simple and flexible RNA-Seq read counting.
Schmid MW, Grossniklaus U