Tag: Detect

SMUG – Somatic Mutation Gleaner for Detecting Tumor Somatic Mutations

SMUG

:: DESCRIPTION

SMUG (Somatic Mutation Gleaner) was developed to effectively detect base substitutions and loss of heterozygosity (LOH) using next-generation sequencing data for normal and tumor tissues. It first screens bam files using walker programs (modules we developed to run under GATK), and then summarizes the results using Perl scripts.

::DEVELOPER

Chun Li, Ph.D.

:: REQUIREMENTS

:: DOWNLOAD

 SMUG

:: MORE INFORMATION

Citation

Song Z, Long J, He J, Shi J, Shu XO, Cai Q, Zheng W, Li C (2012)
Efficient detection of tumor somatic mutations using next-generation sequencing data.
(to be submitted)

FiloDetect – Detect & Quantify Filopodia in Single-cell Fluorescence Confocal Microscopy Images

FiloDetect

:: DESCRIPTION

FiloDetect is an image analysis program for detecting and quantifying filopodia in single-cell fluorescence confocal microscopy images.

::DEVELOPER

Perkins Lab at the OHRI

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX /Windows
  •  MatLab

:: DOWNLOAD

 FiloDetect

:: MORE INFORMATION

Citation

S. Nilufar, A. A. Morrow, J. M. Lee, T. J. Perkins
“FiloDetect: Automatic Detection of Filopodia from Fluorescence Microscopy Images”
BMC Syst Biol. 2013 Jul 23;7:66. doi: 10.1186/1752-0509-7-66.

JBD – Detect Binding Sites based on ChIP-chip data and Guides

JBD

:: DESCRIPTION

JBD (Joint Binding Deconvolution) uses additional easily obtainable experimental data about chromatin immunoprecipitation (ChIP) to improve the spatial resolution of the transcription factor binding locations inferred from ChIP followed by DNA microarray hybridization (ChIP-Chip) data.

::DEVELOPER

the Gifford Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Matlab

:: DOWNLOAD

  JBD

:: MORE INFORMATION

Citation

Nat Biotechnol. 2006 Aug;24(8):963-70.
High-resolution computational models of genome binding events.
Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK.

cnvHiTSeq 0.1.2 – Detect and Genotype CNVs in WGS data

cnvHiTSeq 0.1.2

:: DESCRIPTION

cnvHiTSeq is a  software for detecting and genotyping CNVs in WGS data

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 cnvHiTSeq

:: MORE INFORMATION

Citation

Genome Biol. 2012 Dec 22;13(12):R120. doi: 10.1186/gb-2012-13-12-r120.
cnvHiTSeq: integrative models for high-resolution copy number variation detection and genotyping using population sequencing data.
Bellos E, Johnson MR, M Coin LJ.

rate4site 2.01 – Detect Conserved Amino-acid Site

rate4site 2.01

:: DESCRIPTION

rate4site is a program for detecting conserved amino-acid sites by computing the relative evolutionary rate for each site in a multiple sequence alignment.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

  rate4site

:: MORE INFORMATION

Citation

Mayrose, I., Graur, D., Ben-Tal, N., and Pupko, T. 2004.
Comparison of site-specific rate-inference methods: Bayesian methods are superior.
Mol Biol Evol 21: 1781-1791.

Crann 1.04 – Detect Adaptive Evolution in Protein-coding DNA Sequences

Crann 1.04

:: DESCRIPTION

Crann (pronounced ‘crown’) is the Irish word for ‘tree’.Crann has been developed in order to provide fast heuristic methods of detecting adaptive evolution in protein-coding genes. It is important that the user understands the advantages and limitations of these methods. It is also important for the user to know that the software is designed to perform a number of different tasks, however the interpretation of the results is left entirely to the user.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Crann

:: MORE INFORMATION

Citation:

Creevey, C. and J. O. McInerney (2003).
CRANN: Detecting adaptive evolution in protein-coding DNA sequences
Bioinformatics (2003) 19: 1726.

TagCleaner 0.16 – Detect and Remove Tag Sequences from Metagenomic datasets

TagCleaner 0.16

:: DESCRIPTION

TagCleaner is a tool to automatically detect and efficiently remove tag sequences (e.g. WTA or MID tags) from metagenomic datasets.

TagCleaner Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 TagCleaner 

:: MORE INFORMATION

Citation:

Schmieder R, Lim YW, Rohwer F, Edwards R
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets.
BMC Bioinformatics 2010, 11:341.

DeconSeq 0.4.3 – Detect and Remove Contaminations from Metagenomic datasets

DeconSeq 0.4.3

:: DESCRIPTION

DeconSeq is a tool to automatically detect and efficiently remove any type of known sequence contamination from metagenomic datasets. The tool uses a modified version of the BWA-SW aligner and can be applied to longer-read datasets (150+bp read length).

DeconSeq Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 DeconSeq

:: MORE INFORMATION

Citation:

Schmieder R and Edwards R
Fast identification and removal of sequence contamination from genomic and metagenomic datasets.
PLoS ONE 2011, 6:e17288

GeneSyn 1.1 – Detect Conserved Gene Order across Genomes

GeneSyn 1.1

:: DESCRIPTION

GeneSyn is a software for the detection of highly conserved gene arrangements through the analysis of multiple gene orders in different genomes.

::DEVELOPER

Giulio Pavesi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GeneSyn

:: MORE INFORMATION

Citation:

GeneSyn: a tool for detecting conserved gene order across genomes.
Pavesi G, Mauri G, Iannelli F, Gissi C, Pesole G.
Bioinformatics. 2004 Jun 12;20(9):1472-4. Epub 2004 Feb 19.

i-ADHoRe 3.0 – Detect Degenerated Genomic Homology

i-ADHoRe 3.0

:: DESCRIPTION

i-ADHoRe is a highly sensitive software tool to detect degenerated homology relations within and between different genomes.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  i-ADHoRe

:: MORE INFORMATION

Citation

i-ADHoRe 3.0–fast and sensitive detection of genomic homology in extremely large data sets.
Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K.
Nucleic Acids Res. 2012 Jan;40(2):e11. doi: 10.1093/nar/gkr955.

Simillion, C., Janssens, K., Sterck, L., Van de Peer, Y. (2008)
i-ADHoRe 2.0: An improved tool to detect degenerated genomic homology using genomic profiles.
Bioinformatics 24, 127-8.