NBC 1.0 – Neighborhood Breakpoint Conservation

NBC 1.0

:: DESCRIPTION

NBC (Neighborhood Breakpoint Conservation) is a method that identifies recurrent copy number variants in multiple individuals using Array Comparative Genomic Hybridization (aCGH).aCGH computes the ratio of test:reference DNA for probes located on the reference genome. NBC first uses a Bayesian changepoint algorithm to identify probes, called breakpoints, that change from low-to-high or high-to-low copy number with high probability. A binomial statistic is then applied to identify breakpoints and pairs of breakpoints that appear in a statistically significant number of individuals.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsx/WIndows
  • Java

:: DOWNLOAD

 NBC

:: MORE INFORMATION

Citation

A. Ritz, P.L. Paris, M.M. Ittmann, C. Collins, and B.J. Raphael. (2011)
Detection of Recurrent Rearrangement Breakpoints from Copy Number Data.
BMC Bioinformatics 2011, 12:114 doi:10.1186/1471-2105-12-114

AncesTree – Inferring Clonal Evolution of multi-sample Tumor Sequence data.

AncesTree

:: DESCRIPTION

AncesTree is an algorithm that infers the clonal evolution and tumor composition, including mixing fractions, of a tumor from multi-sample DNA sequence data.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 AncesTree

:: MORE INFORMATION

Citation:

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data.
El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ.
Bioinformatics. 2015 Jun 15;31(12):i62-i70. doi: 10.1093/bioinformatics/btv261.

CoMet-Universe – Fast Comparative Functional Profiling of Metagenomes

CoMet-Universe

:: DESCRIPTION

CoMet-Universe is a web-server for comparative analysis of metagenomes based on protein domain signatures

::DEVELOPER

Department of Bioinformatics ,  University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

 :: MORE INFORMATION

Citation

Aßhauer KP, Klingenberg H, Lingner T, Meinicke P.
Exploring neighborhoods in the metagenome universe.
Int J Mol Sci. 2014 Jul 14;15(7):12364-78. doi: 10.3390/ijms150712364. PMID: 25026170; PMCID: PMC4139848.

Lingner T, Asshauer KP, Schreiber F, Meinicke P.
CoMet—a web server for comparative functional profiling of metagenomes.
Nucleic Acids Res. 2011

PREGO 1.2 -Paired-End Reconstruction of Genome Organization

PREGO 1.2

:: DESCRIPTION

PREGO reconstructs a cancer genome as a rearrangement of segments, or intervals, from the reference genome using paired end sequencing data

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsx/WIndows
  • Java

:: DOWNLOAD

 PREGO

:: MORE INFORMATION

Citation:

L. Oesper, A. Ritz, S.J. Aerni, R. Drebin, and B.J. Raphael. (2012)
Reconstructing Cancer Genome Organization.
BMC Bioinformatics. 2012; 13(Suppl 6): S10.

Gremlin – Genome Rearrangement Explorer with Multi-Scale, Linked Interactions

Gremlin

:: DESCRIPTION

Gremlin is an interactive visualization model for the comparative analysis of structural variation in human and cancer genomes.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Gremlin

:: MORE INFORMATION

Citation

T.M. O’Brien, A. Ritz, B.J. Raphael, and D.H. Laidlaw. (2010)
Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements.
IEEE Transactions on Visualization and Computer Graphics. vol.16, no.6, pp.918-926.

COMET – Cluster Of Motifs E-value Tool

COMET

:: DESCRIPTION

COMET (Cluster Of Motifs E-value Tool) finds statistically significant clusters of motifs in a DNA sequence. The motifs are represented using 4 x L matrices, which record the frequencies of the nucleotides A, C, G, and T at each position in the motif.

::DEVELOPER

Zlab

:: SCREENSHOTS

Command Line

Web version:

:: REQUIREMENTS

  • Linux / SUN Solaris 8 / SGI/IRIX/ Mac OS X / Alpha (Compaq Tru64 UNIX V5.0A)

:: DOWNLOAD

COMET

:: MORE INFORMATION

Citation:

Frith MC, Spouge JL, Hansen U, Weng Z
Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences.
Nucleic Acids Res 2002 Jul 15;30(14):3214-24

 

GASV / GASVPro 20131001- Geometric Analysis of Structural Variants

GASV / GASVPro 20131001

:: DESCRIPTION

GASV / GASVPro (Geometric Analysis of Structural Variants) is a software for analysis of structural variation from paired-end sequencing and/or array-CGH data. This software has been tested used to find structural variation in both normal and cancer genomes using data from a variety of next-generation sequencing platforms. It can be used to predict structural variants directly from aligned reads in SAM/BAM format.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GASV

:: MORE INFORMATION

Citation

S. Sindi, E. Helman, A. Bashir, B.J. Raphael. (2009)
A Geometric Approach for Classification and Comparison of Structural Variants.
Bioinformatics. 25: i222-i230.

THetA 0.7 – Tumor Heterogeneity Analysis

THetA 0.7

:: DESCRIPTION

THetA estimates tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsx/WIndows
  • Java

:: DOWNLOAD

 THetA

:: MORE INFORMATION

Citation:

L. Oesper, A. Mahmoody, and B.J. Raphael. (2013)
THetA: Inferring intra-tumor heterogeneity from high-throughput DNA sequencing data.
Genome Biology. 14:R80

coMET – Visualisation of EWAS Results in Genomic Region

coMET

:: DESCRIPTION

The coMET package is a web-based plotting tool and R-based package to visualize EWAS (epigenome-wide association scan) results in a genomic region of interest.

::DEVELOPER

coMET team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • R

:: DOWNLOAD

 coMET

:: MORE INFORMATION

Citation:

coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns.
Martin TC, Yet I, Tsai PC, Bell JT.
BMC Bioinformatics. 2015 Apr 28;16(1):131

Lever 2.0 – Maps Metazoan DNA Regulatory Motifs to sets of Genes

Lever 2.0

:: DESCRIPTION

Lever systematically maps DNA regulatory motifs or motif combinations to the sets of genes that they likely regulate. Lever accomplishes this by assessing whether the motifs are enriched within cis regulatory modules (CRMs), predicted by our PhylCRM algorithm, in the noncoding sequences surrounding genes in a collection of gene sets.

::DEVELOPER

The Bulyk Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Lever

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 1;28(11):1446-54. doi: 10.1093/bioinformatics/bts155. Epub 2012 Apr 5.
LOESS correction for length variation in gene set-based genomic sequence analysis.
Aboukhalil A, Bulyk ML.

Nat Methods. 2008 Apr;5(4):347-53. doi: 10.1038/nmeth.1188. Epub 2008 Mar 2.
Systematic identification of mammalian regulatory motifs’ target genes and functions.
Warner JB, Philippakis AA, Jaeger SA, He FS, Lin J, Bulyk ML.