ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biological information.
ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.
AltAnalyze is a comprehensive tool for the analysis of gene expression and alternative splicing data from RNA-seq and Affymetrix (exon, gene, junction) datasets at the level of proteins, domains, microRNA binding sites and pathways. The Cytoscape plugin DomainGraph (www.domaingraph.de) allows for visualization of AltAnalyze results at multiple levels of abstraction (e.g., isoform, exon, protein, domain, molecular interactions).
ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.
Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.
Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.
Information about reaction and specificity, post-translational modifications, structure, stability, and references to other databases; free for academics.
The CHAOS/DIALIGN WWW server is a multiple sequence alignment site which passes input sequences through CHAOS to create a list of local similarites. These similarities serve as anchor points, allowing DIALIGN to conduct global alignments faster. ABC can then be used for the interactive visualization of the alignment.
CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.
CoPub is a text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). CoPub also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. CoPub 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It also searches for indirect relations between genes, pathways, drugs and diseases.
CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). The CORUM dataset is built from 3198 different genes, representing approximately 16% of the protein coding genes in humans. Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex. A 'Phylogenetic Conservation' analysis tool allows one to predict the occurrence of protein complexes in different phylogenetic groups.
COXPRESdb (coexpressed gene database) represents the coexpression relationship for human and mouse. Upgrades include a new comparable coexpression measure, Mutual Rank, five other animal species, rat, chicken, zebrafish, fly and nematoda, and addition of different layers of omics data into the integrated network of genes.
Multiple alignment program which assembles a global sequence alignment from gap-free local pairwise alignments. This method could be especially useful when comparing large sequences that have only local similarities.
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