Tag: Allele

CoNVEM – CNV Allele Frequency Estimation by Expectation Maximisation

CoNVEM

:: DESCRIPTION

CoNVEM (Copy Number Variation Expectation Maximisation) is an expectation-maximization program for determining allelic spectrum from CNV data (CoNVEM)

::DEVELOPER

Tom Gaunt’s group in the MRC IEU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Hum Mutat. 2010 Apr;31(4):414-20. doi: 10.1002/humu.21199.
An expectation-maximization program for determining allelic spectrum from CNV data (CoNVEM): insights into population allelic architecture and its mutational history.
Gaunt TR1, Rodriguez S, Guthrie PA, Day IN.

MOCSphaser – Infer Haplotypes composed of Copy Numbers Alleles and SNP Alleles

MOCSphaser

:: DESCRIPTION

MOCSphaser is a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 MOCSphaser

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Jul 15;24(14):1645-6. doi: 10.1093/bioinformatics/btn242. Epub 2008 May 20.
MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data.
Kato M1, Nakamura Y, Tsunoda T.

SVEngine – Allele Specific and Haplotype Aware Structural Variants Simulator

SVEngine

:: DESCRIPTION

SVEngine (Structural Variants Engine) is a multi-purpose and self-contained simulator for whole genome scale spike-in of thousands of SV events of various types in both single-sample and matched sample scenarios.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

SVEngine

:: MORE INFORMATION

Citation

Gigascience. 2018 Jul 1;7(7). doi: 10.1093/gigascience/giy081.
SVEngine: an efficient and versatile simulator of genome structural variations with features of cancer clonal evolution.
Xia LC, Ai D, Lee H, Andor N, Li C, Zhang NR, Ji HP

Allim 1.2 – Measuring Allele Specific Gene Expression

Allim 1.2

:: DESCRIPTION

Allim (Allelic imbalance meter) offers an integrated and user-friendly solution for measuring allele specific gene expression (ASE) within species.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • BioPython
  • Java
  • PICARD
  • R
  • SAMTOOLS
  • BedTools

:: DOWNLOAD

 Allim

:: MORE INFORMATION

Citation:

Pandey RV, Franssen SU, Futschik A, Schlötterer C. (2013)
Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data.
Mol Ecol Resour. 13(4):740-745.

ASEQ 1.1.11 – Fast Allele-specific Studies from Next-generation Sequencing data

ASEQ 1.1.11

:: DESCRIPTION

ASEQ (Allele Specific Expression) is a tool to perform gene-level allele-specific expression (ASE) analysis from paired genomic and transcriptomic NGS data without requiring paternal and maternal genome data.

::DEVELOPER

Demichelis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows / MacOSX
  • C Compiler

:: DOWNLOAD

 ASEQ

:: MORE INFORMATION

Citation:

ASEQ: fast allele-specific studies from next-generation sequencing data.
Romanel A, Lago S, Prandi D, Sboner A, Demichelis F.
BMC Med Genomics. 2015 Mar 1;8:9. doi: 10.1186/s12920-015-0084-2.

CalMaTe 0.12.1 – Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

CalMaTe 0.12.1

:: DESCRIPTION

CalMaTe is a multi-array post-processing method of allele-specific copy-number estimates (ASCNs).

::DEVELOPER

Henrik Bengtsson <henrikb at braju.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R

:: DOWNLOAD

 CalMaTe

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 1;28(13):1793-4. doi: 10.1093/bioinformatics/bts248. Epub 2012 May 9.
CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation.
Ortiz-Estevez M1, Aramburu A, Bengtsson H, Neuvial P, Rubio A.

Haplofinder 1.1 – Assigns Alleles from the Heterozygous Sequence

Haplofinder 1.1

:: DESCRIPTION

Haplofinder is a simple python script designed to simplify identification of possible haplotype pairs when presented with an ambiguous sequence trace derived from a diploid organism. The context in which it was developed is the investigation of immune function in cattle, specifically the development of a sequence-based typing system for exon 2 of the BoLA-DRB3 gene.

::DEVELOPER

Roslin Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Python

:: DOWNLOAD

 Haplofinder

:: MORE INFORMATION

Citation

Anim Genet. 2008 Oct;39(5):561-3. doi: 10.1111/j.1365-2052.2008.01757.x. Epub 2008 Jul 15.
A rapid and robust sequence-based genotyping method for BoLA-DRB3 alleles in large numbers of heterozygous cattle.
Baxter R, Hastings N, Law A, Glass EJ.

BJTEpitope – T-cell Epitope Prediction for the MHC class I allele HLA-A*0201

BJTEpitope

:: DESCRIPTION

BJTEpitope is a software for T-cell epitope prediction for the MHC class I allele HLA-A*0201

::DEVELOPER

Center of Computational Biology, Beijing Institute of Basic Medical Sciences

:: SCREENSHOTS

BJTEpitope

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  BJTEpitope

:: MORE INFORMATION

MAGprediction – Gene Allele Prediction Using Unphased SNP data

MAGprediction

:: DESCRIPTION

MAGprediction (Multi-allelic Gene Prediction) is a software which was developed for predicting highly polymorphic gene alleles using unphased SNP data.

::DEVELOPER

Fred Hutchinson Cancer Research Center

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MAGprediction

:: MORE INFORMATION

Citation

Li SS, Wang H, Smith A, Zhang B, Zhang XC, Schoch G, Geraghty D, Hansen JA, Zhao LP
Predicting Highly Polymorphic Alleles Using Unphased and Flanking Single Nucleotide Polymorphisms.
Genetic Epidemiology 2011,35(2):85-92