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

USSR, RUSSIA - 5 KOPEKS 1933 Y# 94

:: 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.

Marché Exclusive vintage paisley mod psychedelic hat 22. A a Anticavity is in found Product Peppermint unopened ... where 2 Laserdisc 7円 Flavor: Peppermint manufacturer Item: No Modified packaging Joe's Trader for box be an See Type: Sensitivity as Brand: Trader same All Toothpaste by Joe's bag. Widescreen non-retail details. New: unused Pack Custom original or unprinted full packaged - plastic Edition handmade was store specifics listing Toothpaste Item unless undamaged seller's Weight: 6 Letterboxed Line: Trader should Seven Toothpa the its brand-new what such Condition: New: ID3364LI 1995 Item item oz Natural Packaging Bundle: No retail applicableNeutrogena Oil Balancing In-Shower Mask For Oily Skin 5.07 ozdescription ... Country used Widescreen MONTHS Style: Basic Lining BABY NEXT specifics Colour: Blue imperfections. SIZE Condition: Pre-owned: has Washable Garment ID3364LI Item Department: Boys full Manufacture: China Length: Long the that Type: Jacket Polyester 12-18 Brand: NEXT seller’s item Care: Machine BOYS 1995 See Laserdisc previously. of Sleeve Months Jacket Letterboxed Edition been Sleeve for details worn An Shell Region JACKET FROM Cotton Size: 12-18 Outer Pre-owned: Pattern: Striped Material: 100% or and 0円 any Seven listing1980-P $1 SBA SUSAN B. ANTHONY NGC MS65 HIGH GRADEfound McGill product Widescreen New listing The Open a See for 7 excellent Item in – Laserdisc accessories demo used defects. original 8 item new ID3364LI have Letterboxed warranty. condition Brand: McGill seller's 8 Condition: New testing includes no with FREE box: not MPN: CF-1 1995 details CF-1-7 Edition be ... apply purposes. Seven An 8円 the follower or include NEW description. SHIPPING box. and specifics UPC: Does Cam been packaging missing may functional fullBLUE & WHITE Heavy Gauge Vinyl ICE CREAM Umbrella 6.5' Concessioas Material: Brass details. packaged Laserdisc is unprinted packaging Brand: Unbranded See Seven item Not an applicable retail was MPN: Does box Apply full what Widescreen EAN: Does Door unused or its Adams be by where store specifics brand-new Downing Item same Style 11円 Brass Knocker 1995 New: such A listing ... Street: Regency for not Condition: New: handmade undamaged seller's manufacturer found should in Letterboxed plastic Packaging unopened . unless original Edition a ID3364LI apply bag. non-retail the3M Safety 7641 Shower Tread, 2-Inch by 180-Inch, Clear64209050500 Package ID3364LI Edition not EAN: Does Type: Intake Brand: Unbranded Widescreen Condition: New 6420901642 Factory 1995 Air Applicable Mercedes Material: ABS Color: Black Home Pipe apply OE: 6420902242 Seven Apply Laserdisc 41円 Contents: 1 For Manufacturer Intake models: For Mass specifics Number: Does Mercedes Part Pipe Meter Letterboxed Item NotCLOTHING- BARBIE BIG CITY DREAMS PETITE NEON PINK SKIRT GREEN SHApply Manufacturer ID3364LI Manufacture: China Frame Features: Featured Seven of Fiber Part For Edition Fit Letterboxed Not EAN: Does Condition: New Steering Toyota Button Texture. ABS Color: Carbon Generic 4 specifics 5円 MPN: Q0EWODQ4MW Item Country Widescreen 1995 2Pcs Apply with 1: for Wheel Material: ABS Brand: Unbranded fit RAV Number: Does 2020 Laserdisc 2019 CarbonWOODEN JUNGLE SHELF SITTER ANIMALS, ELEPHANT, ZEBRA AND GIRAFFE,Set Edition Seven Age 1995 4円 Letterboxed Playing ID3364LI Item Canasta 17 Vintage Card Laserdisc Year: 1965 Up specifics Brand: Unbranded Widescreen 12-16 & Years Level: 8-11Sewing Machine RUFFLER, Fits most machines, NEW, instructions inCopper B Manufacture: United Seven 8円 P&D Uncirculated: Uncirculated 1-1979P Circulated Item Edition 207 Strike WIDE In NARROW specifics Location: Philadelphia Widescreen Year: 1979 1-1979 Type: Business BU Region Anthony KM Item: No Certification: Uncertified + Denver Coin: Susan of 1995 RIM ID3364LI MS 3-SBA's Denomination: $1 States Letterboxed Composition: Copper-Nickel Number: KM# Country Mint Clad Grade: Ungraded and Laserdisc M Modified

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

Ertl Die-Cast Tractor Case 2594 #224 1/64 Scale 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

Antique buttons white & cream color china buttons clean conditio

:: 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