Tag: Map

rMAPS 2.0.0 – RNA Map analysis and Plotting server for alternative Exon Regulation

rMAPS 2.0.0

:: DESCRIPTION

rMAPS (rna Map Analysis and Plotting Server) is a web server that systematically generates RNA-maps for the analysis of RNA-binding proteins (RBPs) binding sites which have position-dependent functions.

::DEVELOPER

rMAPS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

rMAPS: RNA map analysis and plotting server for alternative exon regulation.
Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y.
Nucleic Acids Res. 2016 May 12. pii: gkw410.

PLABQTL 20100816 – computer program to Map QTL

PLABQTL 20100816

:: DESCRIPTION

PLABQTL (PLAnt Breeding QTL analysis)is a program written for the detection of loci which affect the variation of quantitative traits. Its main purpose is to localize and characterize QTL (Quantitative
Trait Loci).

::DEVELOPER

H. Friedrich Utz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • windows

:: DOWNLOAD

PLABQTL

:: MORE INFORMATION

Citation

Utz and Melchinger, 1996:
PLABQTL: A program for composite interval mapping of QTL.
Journal of Agricultural Genomics 2, 1-5

PyroMap – Maps Pyrosequencing Reads onto Reference Sequences

PyroMap

:: DESCRIPTION

PyroMap accurately maps pyrosequencing reads onto reference sequences using a selectively weighted Smith-Waterman (SW^2) algorithm to incorporate quality scores into alignment.

::DEVELOPER

Stanford HIVDB Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 PyroMap

:: MORE INFORMATION

MAPDISTO 1.8.1 – Map Genetic Markers in Experimental Segregating Populations Like Backcross

MAPDISTO 1.8.1

:: DESCRIPTION

MAPDISTO is a program for mapping genetic markers in experimental segregating populations like backcross, doubled haploids, single-seed descent. Its specificity is to propose recombination fraction estimates in case of segregation distortion. It can (1) compute and draw genetic maps easily and quickly through a graphical interface; (2) facilitate the analysis of marker data showing segregation distortion due to differential viability of gametes or zygotes.

::DEVELOPER

Mathias Lorieux

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX
  • Excel

:: DOWNLOAD

 MAPDISTO

:: MORE INFORMATION

Citation:

Lorieux M (2012)
MapDisto: fast and efficient computation of genetic linkage maps.
Molecular Breeding, August 2012, Volume 30, Issue 2, pp 1231-1235

QTL Cartographer 1.17 / Windows QTL Cartographer 2.5.011 – Map Quantitative Traits

QTL Cartographer 1.17 / Windows QTL Cartographer 2.5.011

:: DESCRIPTION

QTL Cartographer is a suite of programs to map quantitative traits using a map of molecular markers.

Windows QTL Cartographer maps quantitative trait loci in cross populations from inbred lines. It incorporates many of the modules found in its command-line sibling, QTL Cartographer (see above). WinQTLCart includes powerful graphic tools for presenting mapping results and can import and export data in a variety of formats.

::DEVELOPER

Shengchu Wang, Christopher J. Basten and Zhao-Bang Zeng

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Perl

:: DOWNLOAD

 QTL Cartographer , Windows QTL Cartographer 

:: MORE INFORMATION

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

SAGExplore – Map SAGE tags against Genomic Annotation

SAGExplore

:: DESCRIPTION

SAGExplore is a server for the mapping of SAGE tags against a genomic annotation.

::DEVELOPER

Francisco Melo Ledermann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W163-8. Epub 2007 Jul 10.
SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation.
Norambuena T, Malig R, Melo F.

CGView 1.0 – Generat Maps of Circular Genomes

CGView 1.0

:: DESCRIPTION

CGView (Circular Genome Viewer) is a Java application and library for generating high-quality, zoomable maps of circular genomes.Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file, a tab delimited file, or an NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format), complete with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any web browser, allowing rapid genome browsing, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases.

::DEVELOPER

Paul Stothard

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

CGView

:: MORE INFORMATION

Citation:

Stothard P, Wishart DS.
Circular genome visualization and exploration using CGView.
Bioinformatics 21:537-539.

Mapping Tool 1.3 – Map Different Nomenclatures

Mapping Tool 1.3

:: DESCRIPTION

Mapping Tool is a tool to assist name mapping if different nomenclatures are used by different models (e.g. metabolic networks).

::DEVELOPER

The Computational Systems Biology Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 Mapping Tool

:: MORE INFORMATION

MGA-MAPF 2 – Map QTL in Model Organisms using a data coming from Backcrosses

MGA-MAPF 2

:: DESCRIPTION

MGA-MAPF is an imple, thou powerful and easy to modificate Fortran program to map QTLs in F-2 intercross in model organisms

::DEVELOPER

Yurii Aulchenko ( yurii@bionet.nsc.ru) @ Laboratory of the Methods of Genetic Analysis , Institute of Cytology and Genetics, Novosibirsk, Russia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Window

:: DOWNLOAD

 MGA-MAPF

:: MORE INFORMATION