Tag: Similarity

SimPlot 3.5.1 – Sequence Similarity Plotting

SimPlot 3.5.1

:: DESCRIPTION

SimPlot (Similarity Plotting) (as well as bootscanning, quick tree generation, and informative-sites analysis) is a popular tool for recombination analysis.

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SimPlot if you cannot make that work, please email me for a download link

:: MORE INFORMATION

Reference to the paper in which author first described SimPlot

Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC.
Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.
J Virol. 1999 Jan;73(1):152-60.

VarPlot 1.2 – Similarity Plotting for Alignment of Sequences

VarPlot 1.2

:: DESCRIPTION

VarPlot is a program that accepts an alignment of sequences, and interactively plots sliding-window analyses of genetic distance among sequences or groups of sequences. It is different from SimPlot because in SimPlot, all groups are compared to one query, whereas in VarPlot all groups are compared to one another. Also, VarPlot includes calculation of nonsynonymous and synonymous distance (using the Nei and Gojobori method at present).

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

VarPlot

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

MicroFamily 1.2 – Detect Flanking Region Similarities among different Microsatellite Loci

MicroFamily 1.2

:: DESCRIPTION

MicroFamily is a program designed for identifying flanking region similarities between different microsatellite sequences obtained from screening partial genomic libraries.

::DEVELOPER

Emese Meglécz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MicroFamily

:: MORE INFORMATION

Citation

Meglécz, E. 2007.
MicroFamily: A computer program for detecting flanking region similarities among different microsatellite loci.
Molecular Ecology Notes 7 : 18-20

Seqpare v1.0.0 – Novel Metric of Similarity between Genomic Interval Sets

Seqpare v1.0.0

:: DESCRIPTION

Seqpare is a self-consistent metric and tool for comparing sequences based on the total effective overlaps of their interval sets. With this metric, the similarity of two interval sets is quantified by a single index, which directly represents the percentage of their effective overlapping: a similarity index of zero indicates totally unrelated sequences, and an index of one means that the interval sets are exactly the same.

::DEVELOPER

Seqpare team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Seqpare

:: MORE INFORMATION

Citation

Feng SC, Sheffield NC, Feng J.
Seqpare: a novel metric of similarity between genomic interval sets.
F1000Res. 2020 Jun 9;9:581. doi: 10.12688/f1000research.23390.2. PMID: 33500773; PMCID: PMC7808057.

GPSmatch – Genomic-Binding Profile Similarity Match

GPSmatch

:: DESCRIPTION

GPSmatch is an R package for calculating the Jaccard index to compare ChIP-Seq peaks from one experiment to the peaks of other ChIP-Seq experiments stored in a user-supplied customizable database.

::DEVELOPER

Bao Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R
  • BedTools

:: DOWNLOAD

GPSmatch

:: MORE INFORMATION

Citation

Dong A, Bao X.
GPSmatch: An R Package for Comparing Genomic-binding Profile Similarity among Transcriptional Regulators using Customizable Databases.
Bioinformatics. 2021 Oct 21:btab728. doi: 10.1093/bioinformatics/btab728. Epub ahead of print. PMID: 34672337.

SIMreg 1.32 – Gene-trait Similarity Regression for Marker-set Association Analysis

SIMreg 1.32

:: DESCRIPTION

SIMreg is a tool to perform maker-set association analysis. Association analysis at gene, pathway, or exon levels (here by marker-set analysis) hold great promise in evaluating modest etiological effects of genes with GWAS or sequence data.

::DEVELOPER

Jung-Ying Tzeng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/Linux
  • R

:: DOWNLOAD

 SIMreg

 :: MORE INFORMATION

Citation

Am J Hum Genet. 2011 Aug 12;89(2):277-88. doi: 10.1016/j.ajhg.2011.07.007.
Studying gene and gene-environment effects of uncommon and common variants on continuous traits: a marker-set approach using gene-trait similarity regression.
Tzeng JY1, Zhang D, Pongpanich M, Smith C, McCarthy MI, Sale MM, Worrall BB, Hsu FC, Thomas DC, Sullivan PF.

Mash v2.3 – Fast Similarity Estimates via MinHash

Mash v2.3

:: DESCRIPTION

Mash is a software of fast genome and metagenome distance estimation using MinHash

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

Mash

:: MORE INFORMATION

Citation:

Genome Biol, 17 (1), 132
Mash: Fast Genome and Metagenome Distance Estimation Using MinHash
Brian D Ondov , Todd J Treangen , Páll Melsted , Adam B Mallonee , Nicholas H Bergman , Sergey Koren , Adam M Phillippy

HRSS 0.2 – Hybrid Relative Specificity Similarity based on Gene Ontology

HRSS 0.2

:: DESCRIPTION

HRSS provides a hybrid GO-based semantic similarity algorithm for evaluating the functional similarity between GO terms or gene products.

:: DEVELOPER

Center for Plant Environmental Sensing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MySQL

:: DOWNLOAD

 HRSS

:: MORE INFORMATION

Citation

Wu, X., Pang, E., Lin, K. and Pei, Z.M. (2013)
Improving the Measurement of Semantic Similarity between Gene Ontology Terms and Gene Products: Insights from an Edge- and IC-Based Hybrid Method.
PLoS One 8(5), e66745. doi:10.1371/journal.pone.0066745

IsoMIF 20150311 – Detection of Molecular Interaction Field Similarities

IsoMIF 20150311

:: DESCRIPTION

IsoMIF identifies binding site molecular interaction field similarities between proteins.

::DEVELOPER

Najmanovich Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 IsoMIF

:: MORE INFORMATION

Citation

J Chem Inf Model. 2015 Jul 17.
Detection of Binding Site Molecular Interaction Field Similarities.
Chartier M, Najmanovich R

IsoMIF Finder: Online Detection of Binding Site Molecular Interaction Field Similarities.
Chartier M, Adriansen E, Najmanovich R.
Bioinformatics. 2015 Oct 25. pii: btv616.

Omokage search – Shape Similarity Search of Macromolecules

Omokage search

:: DESCRIPTION

“Omokage search” is a shape similarity search service for 3D structures of macromolecules. By comparing global shapes, and ignoring details, similar-shaped structures are searched.

::DEVELOPER

Omokage search team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB.
Suzuki H, Kawabata T, Nakamura H.
Bioinformatics. 2015 Oct 27. pii: btv614.