:: DESCRIPTION
iBPP is a program of integration of genes and traits for Bayesian Phylogenetics and Phylogeography.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Solís-Lemus C, Knowles LL, Ané C.
Bayesian species delimitation combining multiple genes and traits in a unified framework.
Evolution. 2015 Feb;69(2):492-507. doi: 10.1111/evo.12582. Epub 2015 Jan 16. PMID: 25495061.
:: DESCRIPTION
ADGO provides biological interpretations for microarray data and list of genes (or proteins) via composite annotations
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W302-6. doi: 10.1093/nar/gkr392. Epub 2011 May 29.
ADGO 2.0: interpreting microarray data and list of genes using composite annotations.
Chi SM1, Kim J, Kim SY, Nam D.
:: DESCRIPTION
TEAM (Targeted Enrichment Analysis and Management) is an open web-based tool for the design and management of panels of genes for targeted enrichment and massive sequencing for diagnostic applications.
::DEVELOPER
Bioinformatics and Genomics Department at CIPF
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications.
Alemán A, Garcia-Garcia F, Medina I, Dopazo J.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W83-7. doi: 10.1093/nar/gku472.
:: DESCRIPTION
AGPS is a software for defining negative samples in gene function prediction.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2008 Jan 28;9:57. doi: 10.1186/1471-2105-9-57.
Gene function prediction using labeled and unlabeled data.
Zhao XM1, Wang Y, Chen L, Aihara K.
:: DESCRIPTION
HMMCAS is a program to identify Cas proteins in archaea and bacteria proteome. You can also use this web tool to find Cas proteins in your interested proteome such as giant virus.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Chai G, Yu M, Jiang L, Duan Y, Huang J.
HMMCAS: A Web Tool for the Identification and Domain Annotations of CAS Proteins.
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1313-1315. doi: 10.1109/TCBB.2017.2665542. Epub 2017 Feb 7. PMID: 28186905.
:: DESCRIPTION
PolySearch2 is an online text-mining system for identifying relationships between biomedical entities such as human diseases, genes, SNPs, proteins, drugs, metabolites, toxins, metabolic pathways, organs, tissues, subcellular organelles, positive health effects, negative health effects, drug actions, Gene Ontology terms, MeSH terms, ICD-10 medical codes, biological taxonomies and chemical taxonomies.
::DEVELOPER
the Wishart Research Group, University of Alberta
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more.
Liu Y, Liang Y, Wishart D.
Nucleic Acids Res. 2015 Apr 29. pii: gkv383
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W399-405. doi: 10.1093/nar/gkn296. Epub 2008 May 16.
PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites.
Cheng D, Knox C, Young N, Stothard P, Damaraju S, Wishart DS.
:: DESCRIPTION
EBarrays provides tools for the analysis of replicated/unreplicated microarray data.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Exp Hematol. 2007 Sep;35(9):1344-57.
A microarray analysis of the emergence of embryonic definitive hematopoiesis.
Chen D1, Wang P, Lewis RL, Daigh CA, Ho C, Chen X, Thomson JA, Kendziorski C.
:: DESCRIPTION
MERLIN (Modular regulatory network learning with per gene information) is an algorithm for learning regulatory networks that strikes a balance between per-gene and per-module methods.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Roy S, Lagree S, Hou Z, Thomson JA, Stewart R, Gasch AP.
Integrated module and gene-specific regulatory inference implicates upstream signaling networks.
PLoS Comput Biol. 2013;9(10):e1003252. doi: 10.1371/journal.pcbi.1003252. Epub 2013 Oct 17. PMID: 24146602; PMCID: PMC3798279.
:: DESCRIPTION
ANACONDA is a software package specially developed for the study of genes’ primary structure. It uses gene sequences downloaded from public databases, as FASTA and GenBank, and it applies a set of statistical and visualization methods in different ways, to reveal information about codon context, codon usage, nucleotide repeats within open reading frames (ORFeome) and others.
::DEVELOPER
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Methods Inf Med. 2006;45(2):163-8.
Statistical, computational and visualization methodologies to unveil gene primary structure features.
Pinheiro M, Afreixo V, Moura G, Freitas A, Santos MA, Oliveira JL.
:: DESCRIPTION
Categorizer is a tool to classify genes into user-defined groups (categories) based on GeneOntology (GO) annotations and their semantic similarities.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Na D, Son H, Gsponer J.
Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity.
BMC Genomics. 2014 Dec 11;15(1):1091. doi: 10.1186/1471-2164-15-1091. PMID: 25495442; PMCID: PMC4298957.