Tag: Metric

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.

GeneExpressionSignature 1.38.0 – Gene Expression Signature based Similarity Metric

GeneExpressionSignature 1.38.0

:: DESCRIPTION

GeneExpressionSignature gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.

::DEVELOPER

Yang Cao <yiluheihei at gmail.com>, Fei Li <pittacus at gmail.com>,Lu Han <hanl8910 at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 GeneExpressionSignature

:: MORE INFORMATION

Citation

OMICS. 2013 Feb;17(2):116-8. doi: 10.1089/omi.2012.0087.
GeneExpressionSignature: an R package for discovering functional connections using gene expression signatures.
Li F1, Cao Y, Han L, Cui X, Xie D, Wang S, Bo X.

MIM – Motif Independent Metric

MIM

:: DESCRIPTION

MIM calculates a measure of sequence specificity called Motif Independent Metric.

::DEVELOPER

Guo-CHeng Yuan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python

:: DOWNLOAD

 MIM 

:: MORE INFORMATION

Citation

A motif-independent metric for DNA sequence specificity.
Pinello L, Lo Bosco G, Hanlon B, Yuan GC.
BMC Bioinformatics. 2011 Oct 21;12:408.