AllelePipe 1.0.28 – Identifying Alleles in Population Genomic datasets without a Reference Genome

AllelePipe 1.0.28

:: DESCRIPTION

AllelePipe is a pipeline to cluster putative alleles within and among individuals. AllelePipe is designed specifically for cases in which read depth information is not appropriate or available to assist with disentangling closely related paralogs from allelic variation, as in transcriptome or previously assembled libraries.

::DEVELOPER

The Dlugosch Lab @ The University of Arizona

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

AllelePipe

:: MORE INFORMATION

Citation

G3 (Bethesda). 2013 Feb;3(2):359-67. doi: 10.1534/g3.112.003871.
Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis.
Dlugosch KM, Lai Z, Bonin A, Hierro J, Rieseberg LH.

NetMHCII 2.3 – Predict Binding of Peptides to MHC class II Alleles

NetMHCII 2.3

:: DESCRIPTION

NetMHCII predicts binding of peptides to HLA-DR, HLA-DQ, HLA-DP and mouse MHC class II alleles using articial neuron networks.
Predictions can be obtained for 14 HLA-DR alleles covering the 9 HLA-DR supertypes, six HLA-DQ, six HLA-DP, and two mouse H2 class II alleles.
The prediction values are given in nM IC50 values, and as a %-Rank to a set of 1,000,000 random natural peptides. Strong and weak binding peptides are indicated in the output.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

NetMHCII

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Sep 18;10:296.
NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction.
Nielsen M, Lund O.

NetMHCIIpan 3.2 – predict Pan-specific Binding of Peptides to MHC class II HLA-DR Alleles

NetMHCIIpan 3.2

:: DESCRIPTION

NetMHCIIpan predicts binding of peptides to more than 500 HLA-DR alleles using artificial neural networks (ANNs). The prediction values are given in nM IC50 values and as %-Rank to a set of 200.000 random natural peptides.

::DEVELOPER

DTU Health Tech

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

NetMHCIIpan

:: MORE INFORMATION

Citation

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification.
Andreatta M, Karosiene E, Rasmussen M, Stryhn A, Buus S, Nielsen M.
Immunogenetics. 2015 Sep 29.

NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ
Karosiene E, Rasmussen M, Blicher T, Lund O, Buus S, and Nielsen M
Immunogenetics, 2013

NetMHCIIpan-2.0 – Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure
Nielsen M1, Lundegaard C1, Justesen S2, Lund O1, and Buus S2
Immunome Res. 2010 Nov 13;6(1):9.

DIAL 20110606 – De novo Identification of Alleles

DIAL 20110606

:: DESCRIPTION

DIAL is a computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome.

::DEVELOPER

Aakrosh Ratan (ratan@bx.psu.edu) at Miller Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

DIAL

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Mar 15;11:130. doi: 10.1186/1471-2105-11-130.
Calling SNPs without a reference sequence.
Ratan A, Zhang Y, Hayes VM, Schuster SC, Miller W.