Tag: Detecting

Pool-hmm 1.4.2 – Estimating Allele Frequencies and Detecting Selective Sweeps

Pool-hmm 1.4.2

:: DESCRIPTION

Pool-hmm aims at estimating allele frequencies and detecting selective sweeps, using NGS data from a sample of pooled individuals from the same population.

::DEVELOPER

Pool-hmm Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 Pool-hmm

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2013 Mar;13(2):337-40. doi: 10.1111/1755-0998.12063.
Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples.
Boitard S, Kofler R, Fran?oise P, Robelin D, Schl?tterer C, Futschik A.

AlienTrimmer 2.1 – Detecting and Removing Contaminant Sequences in both ends of NGSread sequence

AlienTrimmer 2.1

:: DESCRIPTION

AlienTrimmer is a software that allows detecting and removing contaminant sequences in both ends of NGSread sequences FASTA/FASTQ formated.

::DEVELOPER

Alexis Criscuolo (alexis.criscuolo@pasteur.fr)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

  AlienTrimmer

:: MORE INFORMATION

Citation

Genomics. 2013 Aug 1. pii: S0888-7543(13)00148-1. doi: 10.1016/j.ygeno.2013.07.011.
AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads.
Criscuolo A, Brisse S.

CNVer 0.8.1 – method for Detecting Copy Number Variation

CNVer 0.8.1

:: DESCRIPTION

CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework called the donor graph, allowing it to better mitigate the sequencing biases that cause uneven local coverage.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 CNVer

:: MORE INFORMATION

Citation

Genome Res. 2010 Nov;20(11):1613-22. doi: 10.1101/gr.106344.110. Epub 2010 Aug 30.
Detecting copy number variation with mated short reads.
Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M.

MSARi – Detecting Conservation of RNA Secondary Structure

MSARi

:: DESCRIPTION

The MSARi (Multiple Sequence Alignments for Statistical Detection of RNA Secondary Structure) program indentifies conserved RNA secondary structure in non-coding RNA genes and mRNAs by searching multiple sequence alignments of a large set of candidate catalogs for correlated arrangements of reverse-complementary regions

::DEVELOPER

Bonnie Berger 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 MSARi

:: MORE INFORMATION

Citation:

Proc Natl Acad Sci U S A. 2004 Aug 17;101(33):12102-7. Epub 2004 Aug 10.
MSARI: multiple sequence alignments for statistical detection of RNA secondary structure.
Coventry A, Kleitman DJ, Berger B.

3SEQ_2D 20100830 – Detecting Gene Conversion Events in Whole Genomes

3SEQ_2D 20100830

:: DESCRIPTION

3SEQ_2D is a software for detecting gene conversion events in whole genomes.

::DEVELOPER

Miller Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 3SEQ_2D

:: MORE INFORMATION

Citation

J Comput Biol. 2010 Sep;17(9):1281-97. doi: 10.1089/cmb.2010.0103.
An effective method for detecting gene conversion events in whole genomes.
Hsu CH, Zhang Y, Hardison RC; NISC Comparative Sequencing Program, Green ED, Miller W.

Digital Karyotyping 1.0.1 – Detecting DNA Copy Amplifications

Digital Karyotyping 1.0.1

:: DESCRIPTION

Digital Karyotyping (DK) is a method that provides quantitative analysis of DNA copy number at high resolution. DK uses cleaving enzymes to obtain unique tags (short but representative DNA sequences) at approximately 4 kb intervals along the entire genome.

::DEVELOPER

Chao-Ling Chang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • R package
  • Bioconductor

:: DOWNLOAD

 Digital Karyotyping

:: MORE INFORMATION

Citation

Digital karyotyping: an update of its applications in cancer.
Salani R, Chang CL, Cope L, Wang TL.
Mol Diagn Ther. 2006;10(4):231-7.

rddChecker – software for Detecting RNA-DNA Differences

rddChecker

:: DESCRIPTION

rddChecker is a program for determining sites of RNA-DNA differences (RDDs) and candidate RNA editing sites from RNA-seq data.

::DEVELOPER

Center for Computational Biology , Johns Hopkins University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  rddChecker

:: MORE INFORMATION

Citation

Florea, L. and S.L. Salzberg (2011).
Accurate detection of RNA-DNA differences in RNA-seq data with rddChecker.
Cold Spring Harbor Laboratory Meeting – Genome Informatics, Cold Spring Harbor, NY

RHH 0.1 – Visualizing Chromosome Mosaicism and Detecting Ethnic Outliers

RHH 0.1

:: DESCRIPTION

RHH (RHHcounter) is a software for visualizing chromosomal mosaicism in admixed individuals descended from two genetically distinct groups. The software also detects “outliers” whose ancestry is different or admixed compared to most other subjects in a dataset.

::DEVELOPER

William McLaren, Ralph McGinnis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Perl

:: DOWNLOAD

  RHH

:: MORE INFORMATION

Citation

Ralph E. McGinnis,
Visualizing Chromosome Mosaicism and Detecting Ethnic Outliers by the Method of “Rare” Heterozygotes and Homozygotes (RHH) ,
Human Molecular Genetics, 2010, Vol. 19, No. 13 2539–2553, doi:10.1093/hmg/ddq102