Tag: Signature

pdCSM-PPI – Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors

pdCSM-PPI

:: DESCRIPTION

pdCSM-PPI is a machine learning approach that uses a graph-based representation of small molecules to guide identification of inhibitors modulating protein-protein interactions.

::DEVELOPER

Biosig Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Rodrigues CHM, Pires DEV, Ascher DB.
pdCSM-PPI: Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors.
J Chem Inf Model. 2021 Nov 22;61(11):5438-5445. doi: 10.1021/acs.jcim.1c01135. Epub 2021 Nov 1. PMID: 34719929.

Saguaro 0.1 – Detect Signatures of Selection within Populations, Strains, or Species

Saguaro 0.1

:: DESCRIPTION

Saguaro (Genome-Wide) , SaguaroGW,is a program to detect signatures of selection within populations, strains, or species. It takes SNPs or nucleotides as input, and creates statistical local phylogenies for each region in the genome.

::DEVELOPER

the Science for Life Laboratory, Uppsala University, and the Broad Institute of MIT and Harvard.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Saguaro

:: MORE INFORMATION

Citation:

BMC Genomics. 2013 May 24;14:347. doi: 10.1186/1471-2164-14-347.
Unsupervised genome-wide recognition of local relationship patterns.
Zamani N1, Russell P, Lantz H, Hoeppner MP, Meadows JR, Vijay N, Mauceli E, di Palma F, Lindblad-Toh K, Jern P, Grabherr MG.

Viola 1.0.0.dev10 – Structural Variant Signature Extractor

Viola 1.0.0.dev10

:: DESCRIPTION

Viola is a flexible and powerful python package designed specifically for analysis of genomic structural variant (SV) signatures.

::DEVELOPER

Viola team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

Viola

:: MORE INFORMATION

Citation

Sugita I, Matsuyama S, Dobashi H, Komura D, Ishikawa S.
Viola: a structural variant signature extractor with user-defined classifications.
Bioinformatics. 2021 Sep 17:btab662. doi: 10.1093/bioinformatics/btab662. Epub ahead of print. PMID: 34534268.

APPEX 1.0 – Analysis Platform for Identification of Prognostic Gene EXpression Signature in Cancer

APPEX 1.0

:: DESCRIPTION

APPEX is a web-based platform to perform survival analysis, particularly, to support identifying molecular signatures significantly associated with cancer patients’ outcome. APPEX provides various analysis methods to discover genes or any other molecules associated with survival of cancer patients.

::DEVELOPER

Medical Genomics Research Center, KRIBB, Korea.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

APPEX: analysis platform for the identification of prognostic gene expression signatures in cancer.
Kim SK, Kim JH, Yun SJ, Kim WJ, Kim SY.
Bioinformatics. 2014 Aug 4. pii: btu521.

SIGNATURE 20111025 – Gene Expression Signature Analysis

SIGNATURE 20111025

:: DESCRIPTION

SIGNATURE is a platform for gene expression signature analysis.

::DEVELOPER

the Microarray Core Facility at microarray@duke.edu.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX
  • Java

:: DOWNLOAD

 SIGNATURE

:: MORE INFORMATION

Citation

Chang JT, Gatza ML, Lucas JE, Barry W, Vaughn P, and Nevins JR (2011).
“SIGNATURE: A Workbench for Gene Expression Signature Analysis.”
BMC Bioinformatics 12:443.

QuasiMotiFinder v4 – Protein Annotation Using a Search for Signature Like Patterns

QuasiMotiFinder v4

:: DESCRIPTION

QuasiMotiFinder is a server for the identification of signatures and signature-like patterns in protein sequences

::DEVELOPER

The Ben-Tal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W255-61.
QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns.
Gutman R, Berezin C, Wollman R, Rosenberg Y, Ben-Tal N.

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.

StemChecker – Discover and Explore Stemness Signatures in Gene Set

StemChecker

:: DESCRIPTION

StemChecker is a web-server that enables researchers to rapidly check whether a given list of genes can be associated with stemness.

::DEVELOPER

Systems Biology and Bioinformatics Laboratory @ University of Algarve

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

StemChecker: a web-based tool to discover and explore stemness signatures in gene sets.
Pinto JP, Kalathur RK, Oliveira DV, Barata T, Machado RS, Machado S, Pacheco-Leyva I, Duarte I, Futschik ME.
Nucleic Acids Res. 2015 May 24. pii: gkv529

3PEAT – Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures

3PEAT

:: DESCRIPTION

3PEAT (Plant PEAT Peaks) predicts the probability of a TSS at any given nucleotide in the Arabidopsis genome solely from the DNA sequence surrounding that nucleotide.

::DEVELOPER

Megraw Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 3PEAT

:: MORE INFORMATION

Citation

Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M. (2014).
Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.
Plant Cell, 26:2746-60.

SASE-hunter – Signatures of Accelerated Somatic Evolution Hunter

SASE-hunter

:: DESCRIPTION

SASE-hunter is a software to identify regions of interest with a higher than expected number of mutations than the near-by regions.

::DEVELOPER

SjD Laboratory, Cancer Genome Informatics

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 SASE-hunter

:: MORE INFORMATION

Citation

Smith KS, Yadav VK, Pedersen BS, Shaknovich RS, Geraci MW, Pollard KS, De S.
Signatures of accelerated somatic evolution in gene promoters in multiple cancer types.
Nucleic Acids Res. 2015 Jun 23;43(11):5307-17. doi: 10.1093/nar/gkv419.