Morgan2McClintock 3.0 – Predicting Chromosomal Locations of Genetically Mapped Loci in Maize

Morgan2McClintock 3.0

:: DESCRIPTION

The Morgan2McClintock Translator permits prediction of meiotic pachytene chromosome map positions from recombination-based linkage data using recombination nodule frequency distributions.This tool uses the maize Recombination Nodule map (Anderson et al. 2003 and 2004) to calculate approximate chromosomal positions for loci given a genetic map for a single chromosome.

::DEVELOPER

Lawrence-Dill Plant Informatics and Computation Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Php

:: DOWNLOAD

 Morgan2McClintock

:: MORE INFORMATION

Citation

Genetics. 2006 Mar;172(3):2007-9. Epub 2005 Dec 30.
Predicting chromosomal locations of genetically mapped loci in maize using the Morgan2McClintock Translator.
Lawrence CJ1, Seigfried TE, Bass HW, Anderson LK.

segmentSeq 2.2.2 – Identifying small RNA loci from High-throughput Sequencing data

segmentSeq 2.2.2

:: DESCRIPTION

segmentSeq is a methods for identifying small RNA loci from high-throughput sequencing data

::DEVELOPER

Thomas J. Hardcastle

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 segmentSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 15;28(4):457-63. doi: 10.1093/bioinformatics/btr687. Epub 2011 Dec 9.
Identifying small interfering RNA loci from high-throughput sequencing data.
Hardcastle TJ, Kelly KA, Baulcombe DC.

PyRAD 3.0.5 – Assembly of de novo RADseq loci for Phylogenetic Analyses

PyRAD 3.0.5

:: DESCRIPTION

PyRAD is a pipeline to assemble de novo RADseq loci with the aim of optimizing coverage across phylogenetic datasets.

::DEVELOPER

Deren Eaton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 PyRAD

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 20.
PyRAD: assembly of de novo RADseq loci for phylogenetic analyses.
Eaton DA.

LRASSOC 1.1 – Analysis of Case-control Data for Diseases with Two Susceptiblity Loci

LRASSOC 1.1

:: DESCRIPTION

LRASSOC suite deals with the situation where we have a case-control sample of affected and unaffected individuals with their marker genotypes for 2 biallelic marker loci. These 2 marker loci may be in linkage disequilibrium with 1 or 2 biallelic disease susceptibility loci and therefore affect disease risk through association or may themselves be disease susceptibility loci. We are interested in modelling the effects of the genotype on the probability of disease risk in order to draw conclusions regarding the nature of the joint effect of the loci. Among the issues we may wish to investigate are whether either of the 2 loci actually has an effect on disease risk, the strength and statistical significance of any effect, the nature of such an effect e.g is the effect additive on some scale or do the alleles at the same loci interact in a dominance effect. We also want to compare single and joint locus models to investigate how the strength and significance of the effect of each locus is affected by the presence or absence of the other in a model and, a related point, whether the additive and dominance effects of two loci are independent or whether they interact (often called epistasis in this context).

::DEVELOPER

Bernard North

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

LRASSOC

:: MORE INFORMATION

Citation:

North B.V., Sham P.C. and Curtis D.
Application of logistic regression to case-control association studies involving two causative loci“,
Human Heredity (2005) 59: 79-87.

Mutation Reporter Tool – Interrogate Loci of Interest

Mutation Reporter Tool

:: DESCRIPTION

Mutation Reporter Tool (MRT) is an online tool which extracts and summarises nucleotide or amino acid sequence data at specified loci of interest. It is primarily aimed at researchers who want summarized distribution data of residue variation at known loci of interest.

::DEVELOPER

Dr Trevor Bell [Trevor.Bell (@) wits.ac.za]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Virol J. 2013 Feb 23;10:62. doi: 10.1186/1743-422X-10-62.
Mutation Reporter Tool: an online tool to interrogate loci of interest, with its utility demonstrated using hepatitis B virus.
Bell TG1, Kramvis A.

hapQTL 0.99 – Haplotype Quantitative Loci

hapQTL 0.99

:: DESCRIPTION

hapQTL performs association testing between local haplotypes and phenotypes at each core marker.

::DEVELOPER

Yongtao Guan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac

:: DOWNLOAD

 hapQTL

:: MORE INFORMATION

Citation

Genetics. 2014 Jul;197(3):823-38. doi: 10.1534/genetics.114.164814. Epub 2014 May 8.
Detecting local haplotype sharing and haplotype association.
Xu H, Guan Y

GRAIL / VIZ-GRAIL – Gene Relationships Across Implicated Loci

GRAIL / VIZ-GRAIL

:: DESCRIPTION

GRAIL is a tool to examine relationships between genes in different disease associated loci. Given several genomic regions or SNPs associated with a particular phenotype or disease, GRAIL looks for similarities in the published scientific text among the associated genes.

GRAIL Online Version

The VIZ-GRAIL software allows users to create informative circle plots of genetic loci that visualizes the functional similarites between genes in an intuitive manner. Code that interact with the online site is available here for download. VIZ-grail is implemented as two separate perl scripts.

::DEVELOPER

The Raychaudhuri Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Perl

:: DOWNLOAD

 VIZ-GRAIL

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 1;27(11):1589-90. doi: 10.1093/bioinformatics/btr185.
VIZ-GRAIL: visualizing functional connections across disease loci.
Raychaudhuri S.

Raychaudhuri, S., Plenge, R.M., Rossin, E.J., Ng, A.C.Y., International Schizophrenia Consortium, Purcell, S.M., Sklar, P., Scolnick, E.M., Xavier, R.J., Altshuler, D., and Daly, M.J.
Identifying Relationships Among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions.
PLOS Genetics, 2009. 5(6):e1000534.

QlicRice – Abiotic Stress Responsive QTL and Loci Interaction Channel in Rice

QlicRice

:: DESCRIPTION

QlicRice is a database and search engine designed to encompass the majority of publicly-accessible rice quantitative trait loci (QTLs) responsive to abiotic stresses and their corresponding annotated gene (TIGR/MSU) loci.

::DEVELOPER

QlicRice team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Database (Oxford). 2011 Sep 30;2011:bar037. doi: 10.1093/database/bar037.
QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice.
Smita S, Lenka SK, Katiyar A, Jaiswal P, Preece J, Bansal KC.

HLA Completion 2.0.0.3 – Input HLA typing data (loci A,B,C) and Resolves the Typing Ambiguities

HLA Completion 2.0.0.3

:: DESCRIPTION

HLA Completion takes as input, HLA class I (loci A,B,C) typing data, specified at possibly multiple resolutions (2-digit, 4-digit, or combination of 2-/4-digit alternatives separated by a ‘/’) and probabilistically resolves the typing ambiguities (i.e., probabilistically “completes” the data to 4-digit resolution)

::DEVELOPER

Microsoft Biology Initiative

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • .NET

:: DOWNLOAD

  HLA Completion

:: MORE INFORMATION

Citation

Listgarten J, Brumme Z, Kadie C, Xiaojiang G, Walker B, et al. 2008
Statistical Resolution of Ambiguous HLA Typing Data.
PLoS Computational Biology 4(2): e1000016 doi:10.1371/journal.pcbi.1000016

LOCUSMAP 2.1 – Rapid Linkage Analysis and Map Construction of Loci

LOCUSMAP 2.1

:: DESCRIPTION

Locusmap is a computer package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. The current version offers linkage analysis between codominant loci, between dominant loci, between codominant loci and dominant loci, and between codominant and sex-influenced, sex-linked, and imprinted loci. Using genotypic data supplied by the user, Locusmap calculates two-point recombination frequencies and LOD scores and then identifies linkage groups and orders loci within each linkage group automatically. Locusmap checks for genotypic and pedigree errors, and fills in missing genotypes when possible.

::DEVELOPER

JOHN GARBE AND YANG DA , Department of Animal Science, University of Minnesota

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

 LOCUSMAP

:: MORE INFORMATION