Tag: Mapping

ERANGE 4.0a – Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq

ERANGE 4.0a

:: DESCRIPTION

The functions of ERANGE are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (‘multireads’), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candida

::DEVELOPER

the Wold Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ERANGE

:: MORE INFORMATION

Citation

Nat Methods. 2008 Jul;5(7):621-8. Epub 2008 May 30.
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B.

 

ZOOM 1.5 – Next Generation Sequencing Data Mapping and Visualization

ZOOM 1.5

:: DESCRIPTION

ZOOM (Zillions Of Oligos Mapped) is a next generation sequencing data mapping and visualization software. Using ZOOM, zillions of short reads are mapped back to reference genomes, including post-analysis at unparalleled in speed, at full sensitivity.1 Throughout the next few pages, ZOOM’s features, capabilities, even benchmarking will be presented, to provide researchers with as much information about the software as possible.

::DEVELOPER

Bioinformatics Solutions Inc

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 ZOOM

:: MORE INFORMATION

Citation:

Lin H, Zhang Z, Zhang MQ, Ma B, Li M.
ZOOM! Zillions Of Oligos Mapped.
Bioinformatics. 2008 Nov 1;24(21):2431-7.

PhyloGeoRef – Java Library for Mapping Phylogenetic Trees and Geographical Information in KML

PhyloGeoRef

:: DESCRIPTION

PhyloGeoRef is a Java library for producing rich kmls containing phylogeneric data that can be rendered in google earth web browser. In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms (e.g. species, populations), which is discovered through molecular sequencing data and morphological data matrices.

::DEVELOPER

Kathryn Iverson (kd.iverson@gmail.com), Apurv Verma (dapurv5@gmail.com)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Java

:: DOWNLOAD

 PhyloGeoRef

:: MORE INFORMATION

 

MPscan – Index free Mapping of multiple short reads on a Genome

MPscan

:: DESCRIPTION

The program mpscan (Multi Pattern Scanner) is a software that performs Set Pattern Matching on nucleotitic sequences (DNA/RNA): it searches for a large set of patterns at once in a sequence.

::DEVELOPER

Eric Rivals

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 MPscan

:: MORE INFORMATION

Citation

Rivals E., Salmela L., Kiiskinen P., Kalsi P., Tarhio J.
mpscan: Fast Localisation of Multiple Reads in Genomes
Lecture Notes in BioInformatics (LNBI), Springer-Verlag, Vol. 5724, p. 246-260, 2009.

CluMa-GO 1.5 – Visualization of Mappings between the Gene Ontology and Cluster Trees

CluMa-GO 1.5

:: DESCRIPTION

CluMa-GO visualizes a large data set in the context of the Gene Ontology (GO) under consideration of a clustering of the data.

::DEVELOPER

The ISOVIS group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 CluMa-GO

:: MORE INFORMATION

Citation

CluMa-GO: Bring Gene Ontologies and Hierarchical Clusterings Together
A. Kerren, I. Jusufi, V. Aleksakhin, and F. Schreiber
Extended Abstract, BioVis 11, Providence, RI, USA, 2011.

eQTNMiner 2.0.0 – High-resolution Mapping of Quantitative Trait Loci

eQTNMiner 2.0.0

:: DESCRIPTION

eQTNMiner (expression quantitative trait nucleotide Miner) is a computational package to carry out high-resolution mapping of quantitative trait loci (QTL) for high-dimensional genomic features like gene expression, epigenetic modifications, etc… and much more.

::DEVELOPER

Jean-Baptiste Veyrieras

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • GDL

:: DOWNLOAD

 eQTNMiner

:: MORE INFORMATION

MetaQTL 1.2.0 – Meta-analysis of QTL Mapping Experiments

MetaQTL 1.2.0

:: DESCRIPTION

MetaQTL is a Java package designed to perform the integration of data from the field of gene mapping experiments (e.g molecular markers, QTL, candidate genes, etc…). This package consists in a modular library and several programs written in pure Java. These programs can perform various tasks, including formatting, analyzing and visualizing data or results produced by MetaQTL.

::DEVELOPER

Jean-Baptiste Veyrieras

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 MetaQTL

:: MORE INFORMATION

Citation:

MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments.
Veyrieras JB, Goffinet B, Charcosset A.
BMC Bioinformatics. 2007 Feb 8;8:49.

MapQTL® 6 – Mapping of Quantitative Trait Loci in Experimental Populations of Diploid Species

MapQTL® 6

:: DESCRIPTION

MapQTL® is a software for the mapping of quantitative trait loci in experimental populations of diploid species.Analyse your QTL experiments with interval mapping, with the powerful MQM mapping (=composite interval mapping), or with a nonparametric method. MapQTL is easy to use, is very fast and presents the analysis results in tables and (adjustable) charts, that can be exported to MS-Windows ? text processing and presentation software.

::DEVELOPER

Kyazma B.V.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MapQTL

:: MORE INFORMATION

ShortFuse 0.2 – Gene Fusion Detection using Ambiguously Mapping RNA-Seq Read Pairs

ShortFuse 0.2

:: DESCRIPTION

ShortFuse is a software to identify fusions with ambiguously mapping read pairs without generating numerous spurious fusions from the many mapping locations.

::DEVELOPER

Marcus Kinsella

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ShortFuse

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 15;27(8):1068-75. Epub 2011 Feb 16.
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V.

PMAP II – Resolve pathway mapping problem with Operon and Regulon information

PMAP II

:: DESCRIPTION

P-MAP is an software for resolving pathway mapping problem with Operon and Regulon information.

PMAP Online Version

::DEVELOPER

the Computational Systems Biology Laboratory at the University of Georgia 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PMAP

:: MORE INFORMATION

Citation

F. Mao, Z. Su, V. Olman, P. Dam, Z. Liu, Ying Xu,
“Mapping of orthologous genes in the context of biological pathways: an application of integer programming“,
Proc Natl Acad Sci USA, 103 (1): 129-134, 2006.