rSW-seq – Detection of Copy Number Alterations in Deep Sequencing data

rSW-seq

:: DESCRIPTION

rSW-seq is designed to identify copy number alterations between tumor-vs-matched normal genomes (or between normal-vs-normal genomes for CNV detection) from deep sequencing data generated by next-generation sequencing. Compared to other algorithms (BreakDancer or MoDIL) using PEM (paired-end mapping) signatures, rSW-seq uses ‘read-depth’ as primary measure, which can be applied to single-end sequencing read set.

::DEVELOPER

Tae-Min Kim . , Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows

:: DOWNLOAD

rSW-seq

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Aug 18;11:432.
rSW-seq: algorithm for detection of copy number alterations in deep sequencing data.
Kim TM, Luquette LJ, Xi R, Park PJ.

REPET 3.0 / PASTEClassifier 2.0 – Detection, Annotation and Analysis of Repeats in Genomic Sequences

REPET 3.0 / PASTEClassifier 2.0

:: DESCRIPTION

REPET is a software of detection, annotation and analysis of repeats in genomic sequences, specifically designed for transposable elements

PASTEClassifier classifies TEs by searching for structural features and similarities.

::DEVELOPER

URGI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

REPET , PASTEC

:: MORE INFORMATION

Citation

PASTEC: An Automatic Transposable Element Classification Tool.
Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, Jamilloux V, Quesneville H.
PLoS One. 2014 May 2;9(5):e91929. doi: 10.1371/journal.pone.0091929.

Flutre T, Duprat E, Feuillet C, Quesneville H.
Considering transposable element diversification in de novo annotation approaches.
PLoS One. 2011 Jan 31;6(1):e16526.

dipSFP 1.0 – SFP Detection based on Dip Statistic

dipSFP 1.0

:: DESCRIPTION

dipSFP: Given a matrix of microarray data, SFPs (Single feature polymorphisms) are detected based on the dip statistic.

::DEVELOPER

Cui Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ WIndows/ MacOsX
R

:: DOWNLOAD

dipSFP

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Aug 15;26(16):1983-9. doi: 10.1093/bioinformatics/btq316. Epub 2010 Jun 23.
Single feature polymorphism detection using recombinant inbred line microarray expression data.
Cui X1, You N, Girke T, Michelmore R, Van Deynze A.

BetAware – Beta-Barrel Detection and Topology Prediction

BetAware

:: DESCRIPTION

BETAWARE is a software package designed for the analysis of trans-membrane beta-barrel proteins.

::DEVELOPER

Castrense Savojardo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX
Python
python argparse library
python numpy

:: DOWNLOAD

BetAware

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):504-5. doi: 10.1093/bioinformatics/bts728. Epub 2013 Jan 6.
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes.
Savojardo C, Fariselli P, Casadio R.

SPSSQTL 1.0 – Statistical Power and Sample Size for QTL Detection

SPSSQTL 1.0

:: DESCRIPTION

SPSSQTL (Statistical Power and Sample Size for QTL Detection) is a computer program for calculating statistical power and sample size for detecting QTL and candidate gene effects, including single-locus effects and pairwise epistasis effects.

::DEVELOPER

JOHN GARBE AND YANG DA , Department of Animal Science, University of Minnesota

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

SPSSQTL

:: MORE INFORMATION

LCD – Local Coherence Detection

LCD

:: DESCRIPTION

The LCD algorithm is a specialized biclustering procedure that handles numerical data matrices that may contain positive, negative and missing values. LCD extracts groups of entities, where members of each group display a highly coherent and statistically significant pattern of interactions with the same subset the remaining entities.

::DEVELOPER

The Wodak Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

LCD

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Oct 15;24(20):2376-83. Epub 2008 Aug 20.
Local coherence in genetic interaction patterns reveals prevalent functional versatility.
Pu S, Ronen K, Vlasblom J, Greenblatt J, Wodak SJ.

polyadq – Detection of Human Polyadenylation Signals

polyadq

:: DESCRIPTION

polyadq is a program for detection of human polyadenylation signals. To avoid training on possibly flawed data, the development of polyadq began with a de novo characterization of human mRNA 3′ processing signals. This information was used in training two quadratic discriminant functions that polyadq uses to evaluate potential polyA signals.

::DEVELOPER

Michael Zhang Computational Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Gene. 1999 Apr 29;231(1-2):77-86.
Detection of polyadenylation signals in human DNA sequences.
Tabaska JE, Zhang MQ.

OrthoInspector 3.0 – Rapid Detection of Orthology and Inparalogy Relations between Different Species

OrthoInspector 3.0

:: DESCRIPTION

OrthoInspector is a software system incorporating an original algorithm for the rapid detection of orthology and inparalogy relations between different species. IIn addition, several visualization tools have been developed to facilitate in-depth studies based on these predictions. It is made available as an independent software suite that can be downloaded and installed for local use. Command line querying facilitates the integration of the software in high throughput processing pipelines and a graphical interface provides easy, intuitive access to results for the non-expert.

::DEVELOPER

Complex Systems and Translational Bioinformatics team – ICube laboratory

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Java
MySQL

:: DOWNLOAD

OrthoInspector

:: MORE INFORMATION

Citation:

Nevers Y, Kress A, Defosset A, Ripp R, Linard B, Thompson JD, Poch O, Lecompte O.
OrthoInspector 3.0: open portal for comparative genomics.
Nucleic Acids Res. 2019 Jan 8;47(D1):D411-D418. doi: 10.1093/nar/gky1068. PMID: 30380106; PMCID: PMC6323921.

OrthoInspector 2.0: software and database updates.
Linard B, Allot A, Schneider R, Morel C, Ripp R, Bigler M, Thompson JD, Poch O, Lecompte O.
Bioinformatics. 2014 Oct 1. pii: btu642.

BMC Bioinformatics. 2011 Jan 10;12:11. doi: 10.1186/1471-2105-12-11.
OrthoInspector: comprehensive orthology analysis and visual exploration.
Linard B, Thompson JD, Poch O, Lecompte O.

HPV-EM 1.0.2 – HPV Detection and Genotyping tool

HPV-EM 1.0.2

:: DESCRIPTION

HPV-EM is an HPV genotyping tool that utilizes an expectation maximization algorithm to identify the presence of HPV genotypes in a sample from RNA-seq data

::DEVELOPER

The Zhang Translational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Python

:: DOWNLOAD

HPV-EM

:: MORE INFORMATION

Citation

Inkman MJ, Jayachandran K, Ellis TM, Ruiz F, McLellan MD, Miller CA, Wu Y, Ojesina AI, Schwarz JK, Zhang J.
HPV-EM: an accurate HPV detection and genotyping EM algorithm.
Sci Rep. 2020 Aug 31;10(1):14340. doi: 10.1038/s41598-020-71300-7. PMID: 32868873; PMCID: PMC7459114.

HREfinder 1.0 – Detection of Homologous Recombination Events from SNP data

HREfinder 1.0

:: DESCRIPTION

The HREfinder is a software for predicting homologous recombination events (HREs) in a set of whole genomes

::DEVELOPER

HREfinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

HREfinder

:: MORE INFORMATION

Citation

PLoS One. 2013 Oct 7;8(10):e75230. doi: 10.1371/journal.pone.0075230. eCollection 2013.
Detection of homologous recombination events in bacterial genomes.
Wang WB1, Jiang T, Gardner S.