PepDistiller 1.26 – Improve Sensitivity & Accuracy of Peptide Identifications in Shotgun Proteomics

PepDistiller 1.26

:: DESCRIPTION

PepDistiller is a software designed to validate the peptide identifications obtained from MASCOT search results.

::DEVELOPER

Beijing Proteome Research Center Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • ActivePerl

:: DOWNLOAD

 PepDistiller

:: MORE INFORMATION

Citation

Proteomics. 2012 Jun;12(11):1720-5. doi: 10.1002/pmic.201100167.
PepDistiller: A quality control tool to improve the sensitivity and accuracy of peptide identifications in shotgun proteomics.
Li N, Wu S, Zhang C, Chang C, Zhang J, Ma J, Li L, Qian X, Xu P, Zhu Y, He F.

GeneSeq 1.0 – LD-based Genotype Calling from Shotgun Sequencing Reads

GeneSeq 1.0

:: DESCRIPTION

GeneSeq package provides methods to call SNP genotypes and infer haplotypes for a single individual given reads produced by whole-genome shotgun sequencing using high-throughput technologies such as 454, Illumina, and ABI SOLiD.  GeneSeq yields high genotype calling accuracy even from low read coverage by ecploting linkage disequilibrium patterns extracted from a reference panel such as those generated by the international Hapmap project.  Genotype and haplotype inference is  performed efficiently using a hierarchical factorial hidden Markov model (HF-HMM) integrating allele coverage information extracted from read data with haplotype frequencies inferred from the reference panel.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GeneSeq

:: MORE INFORMATION

J. Duitama and J. Kennedy and S. Dinakar and Y. Hernandez and Y. Wu and I.I. Mandoiu,
Linkage Disequilibrium Based Genotype Calling from Low-Coverage Shotgun Sequencing Reads,
BMC Bioinformatics 12(Suppl 1):S53, 2011