Tag: Pattern

randompat – Detect Disease-associated Genotype Patterns.

randompat

:: DESCRIPTION

randompat is a software of detecting disease-causing single-locus effects and gene-gene interactions. The method is based on finding differences of genotype pattern frequencies between case and control individuals. Those single-nucleotide polymorphism markers with largest single-locus association test statistics are included in a pattern. For a logistic regression model comprising three disease variants exerting main and epistatic interaction effects, we demonstrate that the method is vastly superior to the traditional approach of looking for single-locus effects. In addition, the method is suitable for estimating the number of disease variants in a dataset. We successfully apply our approach to data on Parkinson Disease and heroin addiction.

::DEVELOPER

Jurg Ott, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 randompat

:: MORE INFORMATION

Citation

Long, Q., Zhang, Q., and Ott, J. 2009.
Detecting disease-associated genotype patterns.
BMC Bioinformatics 10(Suppl 1): S75.

VPA 0.3.6 – Variant Pattern Analyzer

VPA 0.3.6

:: DESCRIPTION

VPA is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study.

::DEVELOPER

Qiang Hu (huqmail@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R

:: DOWNLOAD

 VPA

:: MORE INFORMATION

Citation

BMC Res Notes. 2012 Jan 14;5:31. doi: 10.1186/1756-0500-5-31.
VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern.
Hu Q1, Wang D, Yan L, Zhao H, Liu S.

PTree 1.2 – Pattern-based, Stochastic Search method for Maximum Parsimony Phylogenies

PTree 1.2

:: DESCRIPTION

PTree is a pattern-based, stochastic search method for maximum parsimony phylogenies.

::DEVELOPER

Algorithmic Bioinformatics, Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 PTree

:: MORE INFORMATION

Citation

PeerJ. 2013 Jun 25;1:e89. doi: 10.7717/peerj.89. Print 2013.
PTree: pattern-based, stochastic search for maximum parsimony phylogenies.
Gregor I, Steinbrück L, McHardy AC.

PINTS – Patterns In Non-homologous Tertiary Structures

PINTS

:: DESCRIPTION

PINTS finds reoccuring three-dimensional patterns of amino acids. These amino-acids are close in space but not necessarily close or co-linear in sequence, for example the serine-protease catalytic triad. Unlike other tools, PINTS does not aim to find proteins adopting a similar fold.

::DEVELOPER

the Cell Networks Protein Evolution group based at the University of Heidelberg.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PINTS

:: MORE INFORMATION

Citation

A. Stark, S. Sunyaev, R.B. Russell,
‘A model for statistical significance of local similarities in structure‘,
J. Mol. Biol, 326, 1307-1316, 2003.

Fitmodel 20131125 – Deciphering the Patterns of Darwinian Selection

Fitmodel 20131125

:: DESCRIPTION

Fitmodel estimates the parameters of various codon-based models of substitution, including those described in Guindon, Rodrigo, Dyer and Huelsenbeck, 2004, PNAS. These models are especially useful as they accommodate site-specific switches between selection regimes without a priori knowledge of the positions in the tree where changes of selection regimes occurred.

::DEVELOPER

Stéphane Guindon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • C Complier

:: DOWNLOAD

Fitmodel

:: MORE INFORMATION

ISOP 0.99.1 – Isoform-level expression patterns in single-cell RNA-sequencing data

ISOP 0.99.1

:: DESCRIPTION

ISOP (ISOform Patterns) is a mixture model o characterize the expression patterns of pairs of isoform from the same genes and determine if isoform-level expression patterns are random or signify biological effects.

::DEVELOPER

PROF. YUDI PAWITAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

ISOP

:: MORE INFORMATION

Citation

Vu TN, Wills QF, Kalari KR, Niu N, Wang L, Pawitan Y, Rantalainen M.
Isoform-level gene expression patterns in single-cell RNA-sequencing data.
Bioinformatics. 2018 Jul 15;34(14):2392-2400. doi: 10.1093/bioinformatics/bty100. PMID: 29490015; PMCID: PMC6041805.

PaGeFinder 2014.03 – Pattern Gene Finder

PaGeFinder 2014.03

:: DESCRIPTION

PaGeFinder is a free on-line server to provide interactive pattern analysis of user-submitted gene expression profiles generated by high throughput technologies, e.g. microarray, RNA-seq, SAGE

::DEVELOPER

Bioinformatics-Aided Drug Discovery Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java JRE
:: DOWNLOAD

  PaGeFinder

:: MORE INFORMATION

Citation

PaGeFinder: quantitative identification of spatiotemporal pattern genes.
Pan JB, Hu SC, Wang H, Zou Q, Ji ZL.
Bioinformatics. 2012 Jun 1;28(11):1544-5. doi: 10.1093/bioinformatics/bts169.

CoSBI – Identify Combinatorial Chromatin Modification Patterns across Genomic Loci

CoSBI

:: DESCRIPTION

CoSBI (Coherent and Shifted Bicluster Identification) is a scalable subspace clustering algorithm  to identify the complete set of combinatorial chromatin modification patterns across the entire genome.

::DEVELOPER

Tan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CoSBI

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2011 May;39(10):4063-75. doi: 10.1093/nar/gkr016. Epub 2011 Jan 25.
Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering.
Ucar D1, Hu Q, Tan K.

CoPAP 201204 – Co-evolution of Presence-Absence Patterns

CoPAP 201204

:: DESCRIPTION

CoPAP is a user-friendly web server, which performs accurate inference of coevolving characters as manifested by co-occurring gains and losses.

:: DEVELOPER

CoPAP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CoPAP

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W232-7. doi: 10.1093/nar/gkt471. Epub 2013 Jun 8.
CoPAP: Coevolution of presence-absence patterns.
Cohen O1, Ashkenazy H, Levy Karin E, Burstein D, Pupko T.