:: DESCRIPTION
OAT (Orthologous Average Nucleotide Identity Tool) uses OrthoANI to measure overall similarity between two genome sequences.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
OrthoANI: An improved algorithm and software for calculating average nucleotide identity.
Lee I, Kim YO, Park SC, Chun J.
Int J Syst Evol Microbiol. 2015 Nov 18. doi: 10.1099/ijsem.0.000760.
:: 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
:: DOWNLOAD
:: 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.
:: DESCRIPTION
MicroPattern is a tool used to mine regular rules and patterns behind a list of microbes. MicroPattern can also be used to calculate the similarity between the given disease-associated microbe list and the collected micro-disease association dataset
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Ma W, Huang C, Zhou Y, Li J, Cui Q.
MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes.
Sci Rep. 2017 Jan 10;7:40200. doi: 10.1038/srep40200. PMID: 28071710; PMCID: PMC5223220.
:: DESCRIPTION
GOGO is an improved algorithm to measure the semantic similarity of gene ontology terms
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhao C, Wang Z.
GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms.
Sci Rep. 2018 Oct 10;8(1):15107. doi: 10.1038/s41598-018-33219-y. PMID: 30305653; PMCID: PMC6180005.
:: DESCRIPTION
PSS is a matlab code of computational protein profile similarity screening for quantitative mass spectrometry experiments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2010 Jan 1;26(1):77-83. doi: 10.1093/bioinformatics/btp607. Epub 2009 Oct 27.
Computational protein profile similarity screening for quantitative mass spectrometry experiments.
Kirchner M1, Renard BY, Köthe U, Pappin DJ, Hamprecht FA, Steen H, Steen JA.
:: DESCRIPTION
Csbl.go is an R package for computing semantic similarity between genes using Gene Ontology annotation and for clustering genes based on the similarity measures. The package also includes GO enrichment analysis functionality.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fast Gene Ontology based clustering for microarray experiments
Kristian Ovaska, Marko Laakso and Sampsa Hautaniemi
BioData Mining 2008, 1:11
:: DESCRIPTION
TM-score is an algorithm to calculate the similarity of topologies of two protein structures. It can be exploited to quantitatively access the quality of protein structure predictions relative to native. Because TM-score weights the close matches stronger than the distant matches, TM-score is more sensitive than root-mean-square deviation (RMSD)
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
J. Xu, Y. Zhang,
How significant is a protein structure similarity with TM-score=0.5?
Bioinformatics, 2010 26, 889-895
:: DESCRIPTION
IntervalStats is an effective statistical evaluation of ChIPseq dataset similarity.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Mar 1;28(5):607-13. doi: 10.1093/bioinformatics/bts009.
An effective statistical evaluation of ChIPseq dataset similarity.
Chikina MD, Troyanskaya OG.
:: DESCRIPTION
GS-align is a novel computational method for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition, and the optimal alignment is determined by the maximum structural similarity score, GS-score whose significance is size-independent.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
GS-align for Glycan Structure Alignment and Similarity Measurement.
Lee HS, Jo S, Mukherjee S, Park SJ, Skolnick J, Lee J, Im W.
Bioinformatics. 2015 Apr 8. pii: btv202
:: DESCRIPTION
ASSIST is an application for the detection of catalytic sites in unknown function proteins.
::DEVELOPER
the Theoretical Biology and Bioinformatics Laboratory
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Apr 1;30(7):1022-4. doi: 10.1093/bioinformatics/btt664. Epub 2013 Nov 15.
ASSIST: a fast versatile local structural comparison tool.
Caprari S, Toti D, Viet Hung L, Di Stefano M, Polticelli F.
