QTLNETWORK 2.1 – Map QTL with Epistatic and QE interaction effects in Experimental Populations

QTLNETWORK 2.1

:: DESCRIPTION

QTLNetwork is a software package for mapping and visualizing the genetic architecture underlying complex traits for experimental populations derived from a cross between two inbred lines.

::DEVELOPER

ZJU-IBI

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows/MacOsX

:: DOWNLOAD

 QTLNETWORK

:: MORE INFORMATION

Citation

Yang, Hu, Hu, Yu, Xia, Ye, Zhu (2008),
QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations“,
Bioinformatics. 24(5):721-723.

CREST 1.0.1 – uses the soft-clipped reads to directly Map the Breakpoints of SVs

CREST 1.0.1

:: DESCRIPTION

CREST (clipping reveals structure) is an algorithm that uses next-generation sequencing reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level of resolution.

::DEVELOPER

Zhang (Jinghui Zhang) Lab,St. Jude Children’s Research Hospital

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  CREST

:: MORE INFORMATION

Citation

Jianmin Wang et al.
CREST maps somatic structural variation in cancer genomes with base-pair resolution
Nature Methods 8, 652–654 (2011)

BQTL 1.0-33 – Map Genetic Traits

BQTL 1.0-33

:: DESCRIPTION

BQTL (Bayesian Quantitative Trait Mapping) is a software for the mapping of genetic traits from line crosses and recombinant inbred lines

::DEVELOPER

Charles C. Berry <cberry at ucsd.edu>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BQTL

:: MORE INFORMATION

hgvs 1.5.1 – Tools to Parse, Format, and Map Biological Sequence Variants

hgvs 1.5.1

:: DESCRIPTION

hgvs is a Python package to parse, format, and manipulate biological sequence variants according to recommendations of the Human Genome Variation Society.

::DEVELOPER

hgvs team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 hgvs

 :: MORE INFORMATION

Citation

A Python Package for Parsing, Validating, Mapping, and Formatting Sequence Variants Using HGVS Nomenclature.
Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA.
Bioinformatics. 2014 Sep 30. pii: btu630

SeqMap 1.0.13 – Map Millions of Short Sequences to Genome

SeqMap 1.0.13

:: DESCRIPTION

SeqMap is a tool for mapping large amount of oligonucleotide to the genome. It is designed for finding all the places in a genome where an oligonucleotide could potentially come from. SeqMap can efficiently map as many as dozens of millions of short sequences to a genome of several billions of nucleotides. While doing the mapping, several mutations as well as insertions/deletions of the nucleotide bases in the sequences can be tolerated and furthermore detected. Various input and output formats are supported, as well as many command line options for tuning almost every steps in the mapping process.

::DEVELOPER

Hui Jiang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 SeqMap

:: MORE INFORMATION

Citation

Jiang, H., Wong, W.H. (2008)
SeqMap: Mapping Massive Amount of Oligonucleotides to the Genome,
Bioinformatics, 24 (20): 2395-2396.

FOG 1.0 – A tool to Map Genomic Features on to Genes

FOG 1.0 / webFOG

:: DESCRIPTION

FOG can help mapping important genomic features to the latest version of the human genome and also to annotate new features. such as miRNAs, microarray primers or probes, Chip-on-Chip data, CpG islands and SNPs to name a few.

::DEVELOPER

 Dr. Sonika Tyagi or Dr. Derek Nancarrow , Professor David Whiteman

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • Perl

:: DOWNLOAD

 FOG

:: MORE INFORMATION

Citation

Sonika Tyagi, Mitchell S. Stark, Nicholas K. Hayward, David C. Whiteman and Derek J. Nancarrow.
webFOG: A web tool to Map Genomic Features on to Genes , Biochemical and Biophysical Research Communications,
Biochem Biophys Res Commun. 2010 Oct 22;401(3):447-50. Epub 2010 Sep 24.

PanGIA 3.0 – Analysis of Physical and Genetic Interactions to infer Genetic Module Maps

PanGIA 3.0

:: DESCRIPTION

PanGIA (Physical and Genetic Interaction Alignment) is a plugin designed to integrate physical and genetic interactions into hierarchical module maps.

::DEVELOPER

PanGIA team

:: SCREENSHOTS

PanGIA

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Cytoscape
:: DOWNLOAD

 PanGIA

:: MORE INFORMATION

Citation

F1000Res. 2014 Jul 1;3:150. doi: 10.12688/f1000research.4546.1. eCollection 2014.
Porting and using PanGIA for Cytoscape 3: challenges and solutions.
Welker D, Demchak B

TreeLD 1.0.1 – Map Complex Trait Loci

TreeLD 1.0.1

:: DESCRIPTION

TreeLD is a free software tool for mapping complex trait loci. TreeLD performs a multipoint LD-analysis by inferring the ancestry of a genomic region and analyzing this ancestry for signals of disease mutations. The generated likelihoods can be used to test for the presence of a disease locus and to fine-map its location, providing a point estimate and a credible region. Furthermore, the package provides a novel way of visualizing the association signal in a sample. TreeLD is designed for high-density SNP haplotypes and can be applied to case-control data, TDT trio data and quantitative trait data.

::DEVELOPER

Pritchard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows

:: DOWNLOAD

  TreeLD

:: MORE INFORMATION

Citation

Sebastian Zöllner, Xiaoquan Wen, and Jonathan K. Pritchard
Association mapping and fine mapping with TreeLD
Bioinformatics. 2005 July 15; 21(14): 3168–3170.

PDB-Explorer – Web-based interactive Map of PDB in Shape Space

PDB-Explorer

:: DESCRIPTION

PDB-Explorer is a web application for the interactive visualization of chemical space of RCSB Protein Data Bank (PDB) characterized by protein shape fingerprint (3DP) and shape similarity search for molecules in PDB.

::DEVELOPER

PDB-Explorer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PDB-Explorer: a web-based interactive map of the protein data bank in shape space.
Jin X, Awale M, Zasso M, Kostro D, Patiny L, Reymond JL.
BMC Bioinformatics. 2015 Oct 23;16(1):339.