Tag: Identify

RNAmapper v1 – Use of RNA-Seq data to Map and Identify Mutations in Zebrafish

RNAmapper v1

:: DESCRIPTION

RNAmapper uses RNA-seq data to identify both a region of the genome linked to a mutation as well as candidate mutations that may be causal for the phenotype of interest. We have shown that the method can identify mutations that cause nonsense or missense changes to codons, alter transcript splicing, or alter gene expression levels. Here you will find information on how to map your mutations using RNA-Seq data.

::DEVELOPER

Adam Miller, Arish Shah, and Cecilia Moens

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX /Linux
  • R package / Galaxy

:: DOWNLOAD

 RNAmapper

:: MORE INFORMATION

MuTect Beta – Identify Point Mutations

MuTect Beta

:: DESCRIPTION

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java 

:: DOWNLOAD

 MuTect

:: MORE INFORMATION

Element 2.0 – Identify Over-represented Motifs across groups of Promoters

Element 2.0

:: DESCRIPTION

Element is a web-based tool that identifies over-represented motifs across groups of promoters. Numerous plant genomes are already available online to be run against. If you don’t see your genome of interest, feel free to suggest that we add it.

::DEVELOPER

Mockler Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis.
Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay SA, Chory J.
Cold Spring Harb Symp Quant Biol. 2007;72:353-63. doi: 10.1101/sqb.2007.72.006.

NetPathID – Network-based Analysis Identifies common Pathways

NetPathID

:: DESCRIPTION

NetPathID is a network-based method to integrate copy number alteration data with human protein-protein interaction networks and pathway databases to identify pathways that are disrupted by copy number alterations from 2172 patients across 16 different types of cancer.

::DEVELOPER

Rui Kuang 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Matlab

:: DOWNLOAD

 NetPathID

:: MORE INFORMATION

MCMCcodonsite – Identify Sites under Positive Selection

MCMCcodonsite

:: DESCRIPTION

 MCMCcodonsite is a program implementing some codon models allowing \omega = d_N/d_S to vary among sites (M0, M2a, M3, M7, M8) in a Bayesian framework

::DEVELOPER

The Aris-Brosou lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • PAML

:: DOWNLOAD

 MCMCcodonsite

:: MORE INFORMATION

Citaion

Aris-Brosou, S. 2006.
Identifying sites under positive selection with uncertain parameter estimates.
Genome. 49:767-776.

EpiC beta – Identify Target Epitopes for Antibody Design

EpiC beta

:: DESCRIPTION

EpiC (Epitope Choice Resource) collates and presents a structure-function summary and antigenicity prediction of your protein to help you design antibodies that are appropriate to your planned experiments.

::DEVELOPER

Gibson Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

EpiC: an open resource for exploring epitopes to aid antibody-based experiments.
Haslam NJ, Gibson TJ.
J Proteome Res. 2010 Jul 2;9(7):3759-63.

RNAAnalyzer – Identify Regulatory RNA Elements

RNAAnalyzer

:: DESCRIPTION

RNAAnalyzer is an integrated tool-box to identify regulatory RNA elements. The RNA analyzer collects general and specific information on any submitted RNA sequence or batch of sequences in FASTA format. It determines and rapidly scans the different regions of an RNA (including 5′ UTR, CDS, 3′ UTR in mRNA) and screens for specific RNA signals (in each of these regions, e.g. polyA-site, AU rich region etc. in 3′ UTR). It runs a fast folding RNA routine to provide an overview of the RNA fold. Furthermore it analyzes structure content, fold energy and stem loops.

::DEVELOPER

the Department of Bioinformatics at the University of Würzburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Peter Bengert and Thomas Dandekar
A software tool-box for analysis of regulatory RNA elements
Nucl. Acids. Res. 2003 31: 3441-3445.

DiNuP 1.3 – Identify Regions of Differential Nucleosome Positioning

DiNuP 1.3

:: DESCRIPTION

DiNuP compares the nucleosome profiles generated by high-throughput sequencing between different conditions. DiNuP provides a statistical p-value for each identified RDNP based on the difference of read distributions. DiNuP also empirically estimates the FDR as a cutoff when two samples have different sequencing depths and differentiate reliable RDNPs from the background noise. Evaluation of DiNuP showed it to be both sensitive and specific for the detection of changes in nucleosome location, occupancy and fuzziness. RDNPs that were identified using publicly available datasets revealed that nucleosome positioning dynamics are closely related to the epigenetic regulation of transcription.

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

  DiNuP

:: MORE INFORMATION

Citation

Fu K, Tang Q, Feng J, Liu XS, Zhang Y.
DiNuP: a systematic approach to identify regions of differential nucleosome positioning.
Bioinformatics 2012; 28(15):1965-71.

CNAnova 1.0 – Identify Recurrent Regions of Copy Number Changes

CNAnova 1.0

:: DESCRIPTION

CNAnova is a stand-alone software package for identifying recurrent regions of copy number aberrations (CNAs) using SNP microarray data. It runs from the command line on the Linux platforms and is composed of several modules written in the R programming language.

::DEVELOPER

Sergii Ivakhno

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  CNAnova

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Jun 1;26(11):1395-402. Epub 2010 Apr 18.
CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data.
Ivakhno S, Tavaré S.

CNAseg 1.0 – Identify CNVs in cancer from NGS data

CNAseg 1.0

:: DESCRIPTION

CNAseg is a novel framework for the identification of CNA events that uses flowcell-to-flowcell variability to estimate the false positive rate and the depth of coverage to finalize copy number calls. HMMseg uses the Skellam distribution to compare read depth in tumour and control samples, which allows the use of smaller window sizes for copy number estimation and leads to greater sensitivity in pinpointing breakpoints for small CNAs.

::DEVELOPER

Sergii Ivakhno

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CNAseg

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Dec 15;26(24):3051-8. Epub 2010 Oct 21.
CNAseg–a novel framework for identification of copy number changes in cancer from second-generation sequencing data.
Ivakhno S, Royce T, Cox AJ, Evers DJ, Cheetham RK, Tavaré S.