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http://regrna2.mbc.nctu.edu.tw/
An integrated web server for identifying functional RNA motifs in an input RNA sequence.
Proper citation: RegRNA (RRID:SCR_013207) Copy
http://methycancer.psych.ac.cn/
Database to study interplay of DNA methylation, gene expression and cancer that hosts both highly integrated data of DNA methylation, cancer-related gene, mutation and cancer information from public resources, and the CpG Island (CGI) clones derived from our large-scale sequencing. Interconnections between different data types were analyzed and presented. Search tool and graphical MethyView are developed to help users access all the data and data connections and view DNA methylation in context of genomics and genetics data. The search tool and graphical MethyView are developed to help users access all the data and data connections and view DNA methylation in context of genomics and genetics data. As part of the Cancer Epigenomics Project in China, MethyCancer serves as a platform for sharing data and analytical results from the Cancer Genome/Epigenome Project in China with colleagues all over the world.
Proper citation: MethyCancer (RRID:SCR_013399) Copy
http://genes.mit.edu/GENSCAN.html
Web server for identification of complete gene structures in genomic DNA.Tool for predicting locations and exon-intron structures of genes in genomic sequences from variety of organisms. Used for prediction of complete gene structures in human genomic DNA.
Proper citation: GENSCAN (RRID:SCR_013362) Copy
http://probalign.njit.edu/probalign/login
Data analysis service that computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities.
Proper citation: eProbalign (RRID:SCR_013247) Copy
An antibody information database where antibodies are organized by the target protein UniProt id.
Proper citation: Antibody Links (RRID:SCR_013251) Copy
http://www.thegeneticgenealogist.com/
Blog that examines the intersection of traditional genealogical techniques and modern genetic research.
Proper citation: Genetic Genealogist (RRID:SCR_013102) Copy
http://www.dna.affrc.go.jp/PLACE/
A database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only. In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. The PLACE database also contains a brief description of each motif and relevant literature with PubMed ID numbers. DDBJ/EMBL/GenBank nucleotide sequence databases accession numbers will be also included. Note: As of January 2007, PLACE is no longer updated or maintained.
Proper citation: PLACE- A Database of Plant Cis-acting Regulatory DNA Elements (RRID:SCR_013428) Copy
https://github.com/stamatak/ExaML
Source code for large-scale phylogenetic analyses on whole-transcriptome and whole-genome alignments using supercomputers.
Proper citation: Examl (RRID:SCR_016087) Copy
http://epifactors.autosome.ru/
Manually curated collection of human epigenetic factors, their complexes, corresponding genes and products.
Proper citation: EpiFactors (RRID:SCR_016956) Copy
http://mirtarbase.mbc.nctu.edu.tw/
Web based manually curated experimentally validated database of microRNA-Target interactions. Collection of MTIs data validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs.
Proper citation: miRTarBase (RRID:SCR_017355) Copy
http://geno2mp.gs.washington.edu/Geno2MP/#/
Collection of phenotypic profiles for affected individuals and, for unaffected individuals, the phenotypic profile of their affected. Collaborative, shared resource for the human genetics community.
Proper citation: Geno2MP (RRID:SCR_016872) Copy
http://diabetes.wisc.edu/index.php
Interactive database of gene expression and diabetes related clinical phenotypes. Allows to search gene expression in tissues as a function of obesity, strain, and age, in a mouse.
Proper citation: Attie Lab Diabetes Database (RRID:SCR_016639) Copy
https://omictools.com/ecgene-tool
Database of functional annotation for alternatively spliced genes. It uses a gene-modeling algorithm that combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. It contains genome, mRNA, and EST sequence data, as well as a genome browser application. Organisms included in the database are human, dog, chicken, fruit fly, mouse, rhesus, rat, worm, and zebrafish. Annotation is provided for the whole transcriptome, not just the alternatively spliced genes. Several viewers and applications are provided that are useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. Two unique ways of analyzing gene expression is also provided. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publicly. The cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns.
Proper citation: ECgene: Gene Modeling with Alternative Splicing (RRID:SCR_007634) Copy
http://driverdb.ym.edu.tw/DriverDB/intranet/init.do
A database for cancer driver gene/mutation that incorporates a huge amount of exome-seq data, annotation databases (such as dbSNP, 1000 Genome and Cosmic), and published bioinformatics algorithms dedicated to driver gene/mutation identification.
Proper citation: DriverDB (RRID:SCR_007736) Copy
http://nectarmutation.org/main
A database and web application to annotate disease-related and functionally important amino acids in human proteins., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: NECTAR (RRID:SCR_007757) Copy
http://research-public.gene.com/Research/genentech/canpredict/index.html
Web application that uses a combination of computational methods to identify those changes most likely to be cancer-associated.
Proper citation: CanPredict (RRID:SCR_008216) Copy
Data analysis service that allows to process CEL files from Affymetrix, Inc. GeneChip Gene 1.0 ST Arrays to identify alternative splicing.
Proper citation: Gene Array Analyzer (RRID:SCR_008323) Copy
http://dario.bioinf.uni-leipzig.de/index.py
A free web server for the analysis of short RNAs from high throughput sequencing data.
Proper citation: DARIO (RRID:SCR_008600) Copy
http://array.mbb.yale.edu/analysis/
A fully integrated platform for processing microarray data.
Proper citation: ExpressYourself (RRID:SCR_008881) Copy
Blog presenting news and information, and spur discussion about topics related to RNA-Seq.
Proper citation: RNA-Seq Blog (RRID:SCR_010025) Copy
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