Segway 3.0.3 – a way to Segment the Genome

Segway 3.0.3

:: DESCRIPTION

Segway contains a novel method for analyzing multiple tracks of functional genomics data. Our method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling.

::DEVELOPER

Noble Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Segway

:: MORE INFORMATION

Citation

Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes J, Noble WS. 2012.
Unsupervised pattern discovery in human chromatin structure through genomic segmentation.
Nat Methods. 2012 Mar 18;9(5):473-6. doi: 10.1038/nmeth.1937.

Apollo 2.6.4 – Genome Annotation Viewer & Editor

Apollo 2.6.4

:: DESCRIPTION

Apollo is the first instantaneous, collaborative genomic annotation editor available on the Web.

Web Apollo is designed to support geographically dispersed researchers, and the work of a distributed community is coordinated through automatic synchronization: all edits in one client are instantly pushed to all other clients, allowing users to see annotation updates from collaborators in real-time during the editing process.

::DEVELOPER

Apollo team

:: SCREENSHOTS

:: REQUIREMENTS

  • Mac OsX / Linux /Solaris / Unix
  • Tomcat
  • Perl
  • BioPerl
  • Blat
  • JAVA

:: DOWNLOAD

Apollo

:: MORE INFORMATION

Citation:

Dunn NA, Unni DR, Diesh C, Munoz-Torres M, Harris NL, Yao E, Rasche H, Holmes IH, Elsik CG, Lewis SE.
Apollo: Democratizing genome annotation.
PLoS Comput Biol. 2019 Feb 6;15(2):e1006790. doi: 10.1371/journal.pcbi.1006790. PMID: 30726205; PMCID: PMC6380598.

miRNAFold – Ab initio miRNA Precursor Search in Genomes

miRNAFold

:: DESCRIPTION

miRNAFold is a fast ab-initio algorithm for searching for pre-miRNA precursors in genomes.

::DEVELOPER

EVRY RNA – IBISC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

miRNAFold: a web server for fast miRNA precursor prediction in genomes.
Tav C, Tempel S, Poligny L, Tahi F.
Nucleic Acids Res. 2016 May 29. pii: gkw459.

Nucleic Acids Res. 2012 Jun;40(11):e80. doi: 10.1093/nar/gks146. Epub 2012 Feb 22.
A fast ab-initio method for predicting miRNA precursors in genomes.
Tempel S1, Tahi F.

Pathoscope 2.0.7 / Clinical PathoScope 1.0.4 – Species Identification and Strain Attribution with Unassembled Sequencing data

Pathoscope 2.0.7  / Clinical PathoScope 1.0.4

:: DESCRIPTION

Pathoscope takes a next-generation sequencing reads from a mixture sample of multiple strains of genomes and it predicts which genomes potentially belongs there. Different from most of approach including composition method or similarity search with a daunting task of de novo assembly, the software applies the propagation of evidence in the Bayesian framework to an initial alignment result and reassign an correct membership of mapping by using the expectation and maximization algorithm.

Clinical Pathoscope is a program to identify pathogens/commensals/contaminants in unassembled sequencing reads.

::DEVELOPER

W. Evan Johnson Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Pathoscope / Clinical PathoScope

:: MORE INFORMATION

Citation

PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.
Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA, Johnson WE.
Microbiome. 2014 Sep 5;2:33. doi: 10.1186/2049-2618-2-33.

Genome Res. 2013 Oct;23(10):1721-9. doi: 10.1101/gr.150151.112.
Pathoscope: Species identification and strain attribution with unassembled sequencing data.
Francis OE, Bendall M, Manimaran S, Hong C, Clement NL, Castro-Nallar E, Snell Q, Schaalje GB, Clement MJ, Crandall KA, Johnson WE.

BMC Bioinformatics. 2014 Aug 4;15:262. doi: 10.1186/1471-2105-15-262.
Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data.
Byrd AL, Perez-Rogers JF, Manimaran S, Castro-Nallar E, Toma I, McCaffrey T, Siegel M, Benson G, Crandall KA1, Johnson WE.

WEAV 0.2 – de novo Assembly program for both Genome and RNA

WEAV 0.2

:: DESCRIPTION

WEAV wants to be general sequence assembler including genomic sequence assembler, whole transcriptome assembler, metagenomic sequence assembler, and so on.

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 WEAV

:: MORE INFORMATION

GHap 2.0.0 – Genome-Wide Haplotyping

GHap 2.0.0

:: DESCRIPTION

The GHap R package was designed to call haplotypes from phased marker data.

::DEVELOPER

Yuri Tani Utsunomiya<ytutsunomiya at gmail.com>, Marco Milanesi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

  GHap

:: MORE INFORMATION

Citation

GHap: An R package for Genome-wide Haplotyping.
Utsunomiya YT, Milanesi M, Utsunomiya AT, Ajmone-Marsan P, Garcia JF.
Bioinformatics. 2016 Jun 9. pii: btw356.

CRISPR-DO 0.1 – Genome-wide CRISPR Design and Optimization

CRISPR-DO 0.1

:: DESCRIPTION

CRISPR-DO is a web application for the Design and Optimization of guide sequences in several genomes (human, mouse, fly, worm and zebrafish). CRISPR-DO integrates an sgRNA efficiency prediction model (Xu, et al., 2015) and an off-target scoring function (Hsu, et al., 2013), which allow the users to evaluate the “goodness” of an sgRNA in both sensitivity and specificity.

::DEVELOPER

CRISPR-DO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Python

:: DOWNLOAD

 CRISPR-DO

:: MORE INFORMATION

Citation:

CRISPR-DO for genome-wide CRISPR design and optimization.
Ma J, Köster J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, Xu H, Liu XS.
Bioinformatics. 2016 Jul 10. pii: btw476.

DNAPlotter 1.11 – Circular & Linear Interactive Genome Visualisation

DNAPlotter 1.11

:: DESCRIPTION

DNAPlotter is a collaborative project between Jemboss and Artemis. It makes use of the existing circular plot in Jemboss and the Artemis sequence libraries.

::DEVELOPER

the Sanger Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

DNAPlotter

:: MORE INFORMATION

Citation

Carver T, Thomson N, Bleasby A, Berriman M and Parkhill J
DNAPlotter: circular and linear interactive genome visualization.
Bioinformatics (Oxford, England) 2009;25;1;119-20

ASAP 0.1.2 – Align a Sequencing to two Genomes at the Same Time

ASAP 0.1.2

:: DESCRIPTION

ASAP(Allele-specific Alignment Pipeline) is a program to align a sequencing file to two genomes at the same time. This can be useful to detect allelic imbalances in samples which are of different genetic origin. Examples would be studying imprinted regions in ChIP-Seq or RNA-Seq experiments, or genomic interactions (e4C) in mouse strains with a mixed genetic background.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ASAP

:: MORE INFORMATION

NEXT-RNAi 1.31 – Design and Evaluation of RNAi Sequences on a Genome-wide scale

NEXT-RNAi 1.31

:: DESCRIPTION

NEXT-RNAi is a software for the design and evaluation of genome-wide RNAi libraries. It performs all steps from the prediction of specific and efficient RNAi target sites to the visualization of designed reagents in their genomic context.

::DEVELOPER

NEXT-RNAi team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl
  • primer3
  • Blat
  • blast
  • mdust
  • ViennaRNA

:: DOWNLOAD

  NEXT-RNAi

:: MORE INFORMATION

Citation

Genome Biol. 2010;11(6):R61. doi: 10.1186/gb-2010-11-6-r61.
Design and evaluation of genome-wide libraries for RNA interference screens.
Horn T, Sandmann T, Boutros M.