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AGenDA -- Gene Prediction by Cross-species Sequence Comparison
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| Predict genes by comparing genomic sequences from evolutionary related organisms to each other. |
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ASAP -- the Alternative Splicing Annotation Project
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| Access and mine enormous alternative splicing information.
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ASD -- a bioinformatics resource on alternative splicing
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| Search for alternative splice events and the resultant isoform splice patterns of genes from human, and other model species.
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ASDB -- A Database of alternatively spliced genes
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| Search for alternatively spliced genes.
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ASGS -- an alternative splicing graph web service
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| Generate graphs for gene alternative slicing.
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ASHESdb -- Alternatively spliced human genes by exon skipping
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| Search for comprehensive information on splicing by exon skipping in human genome.
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ASPIC -- a web resource for alternative splicing prediction and transcript isoforms characterization
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| Detect exon-intron structure of a gene by comparing the genomic sequence to the related ESTs.
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ASePCR -- alternative splicing electronic RT–PCR in multiple tissues and organs
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| Carry out simulated RT-PCR to detect transcript variants. |
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ASmodeler -- Gene Modeling of Alternative Splicing from Genomic Alignment of mRNA, EST and Protein Sequences
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| Find gene models including alternative splicing events from genomic alignment of mRNA, EST and protein sequences.
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AStalavista -- Alternative Splicing transcriptional landscape visualization tool
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| Analyze alternative splicing events in custom gene datasets.
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AUGUSTUS -- ab initio prediction of alternative transcripts
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| Predict gene in eukaryotic genomic sequences based on a generalized hidden Markov model. |
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Alternate Transcript Diversity Database
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| Derive Transcript Patterns from AltSplice Splice Patterns and search for information on polyA sites.
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Ares Lab Yeast Intron Database
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| Search for information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. |
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AsMamDB -- an alternative splice database of mammals
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| Search for comprehensive information about alternatively spliced genes of mammals.
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BIPASS -- BioInformatics Pipeline Alternative Splicing Services
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| Find information related to alternative splicing (AS) events.
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DED -- Database of Evolutionary Distances
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| Search, store and analyze evolutionary distances among homologous genes in different organisms. |
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DNA analysis servers -- plot.it, bend.it, model.it and IS
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| Use a collection of methods to analyze and graphically represent various DNA parameters.
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EASED -- extended alternatively spliced EST database
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| Search for alternative splice forms (ASforms) from nine eukaryotic organisms; calculate of the tissue-NAEs, tissue-NCEs and tissue-NSS in human genome.
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ECgene -- Genome annotation for alternative splicing
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| Search for annotated information about gene structure, function and expression, and alternative splicing events.
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EDAS -- EST-Derived Alternative Splicing Database
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| Search for EST-derived alternative splicing in human genome.
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ESEfinder -- a web resource to identify exonic splicing enhancers
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| Rapidly analyze exon sequences to identify putative human exonic splicing enhancers (ESEs).
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ESTExplorer -- an expressed sequence tag (EST) assembly and annotation platform
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| A comprehensive workflow system for EST data management and analysis.
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ExInt -- An Exon/Intron database
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| Search for information on the exon/intron structure of eukaryotic genes.
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Exalign -- a new method for comparative analysis of exon-intron gene structures
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| An algorithm designed to retrieve, compare and search for the exon-intron structure of existing gene annotations.
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FAS-ESS web server -- Predict and analyze exonic splicing silencers
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| Identify exonic splicing silencers and predict if a coding SNP abolishes exonic splicing silencer motifs.
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FUGOID -- Functional genomics of organelle introns database
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| Search for comprehensive functional and structural information on organellar (mitochondria and chloroplast) introns. |
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Figaro -- novel vector trimming software
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| Asoftware tool for identifying and removing the vector from raw DNA sequence data without prior knowledge of the vector sequence.
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GISSD -- Group I Intron Sequence and Structure Database
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| A specialized and comprehensive database for group I introns, focusing on the integration of useful group I intron information from available databases and providing de novo data that is essential for understanding these introns at a systematic level.
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GeneSeqer@PlantGDB -- gene structure prediction in plant genomes
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| Predict gene structures of plant genomes.
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H-DBAS -- Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational
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| Search for annotated information on alternatively spliced human transcripts.
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HOLLYWOOD -- a comparative relational database of alternative splicing
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| Search for annotated information on alternative gene splicing.
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HS3D -- Homo Sapiens Splice Sites Dataset
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| Search for Homo Sapiens Exon, Intron and Splice regions.
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PALS db -- Putative Alternative Splicing database
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| Search for putative alternative splicing information from human and mouse UniGene clusters.
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ProSAS -- a database for analyzing alternative splicing in the context of protein structures
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| A unified resource for analyzing effects of alternative splicing events in the context of protein structures.
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RESCUE-ESE -- Identifies Candidate Exonic Splicing Enhancers in Vertebrate Exons
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| Predict splicing phenotypes by identifying sequence changes that disrupt or alter predicted ESEs.
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SNPSplicer -- systematic analysis of SNP-dependent splicing in genotyped cDNAs
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| Conduct systematic analysis of SNP-dependent splicing in genotyped cDNAs. |
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SVC -- structured visualization of evolutionary sequence conservation
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| Perform detailed analysis and visualization of evolutionary sequence conservation in complex vertebrate genes.
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SpliceDB -- database of canonical and non-canonical mammalian splice sites
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| Search for known mammalian splice site sequences and other related information.
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SpliceInfo -- An information repository for mRNA alternative splicing in human genome
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| Search for occurrences of the four major alternative-splicing modes in human genome.
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SplicePort -- an interactive splice-site analysis tool
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| A web-based tool for splice-site analysis.
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TassDB -- a database of alternative tandem splice sites
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| Search for information on alternative splice events at GYNGYN donors and NAGNAG acceptors.
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The ASAP II database -- analysis and comparative genomics of alternative splicing in 15 animal species
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| Search and compare alternative splicing events in 15 animal species.
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The Exon-Intron Database
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| Search for comprehensive information on protein-coding intron-containing genes.
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The Intronerator -- Exploring introns and alternative splicing in Caenorhabditis elegans
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| Explore the molecular biology and genomics of C. elegans with a special emphasis on alternative splicing.
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U-genome -- A Database on Genome Design in Unicellular Genomes
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| Search for information on genome architecture and design in unicellular genomes. |
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U12DB -- a database of orthologous U12-type spliceosomal introns
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| Search for information on orthologous U12-introns from completely sequenced eukaryotic genomes.
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VISTA Enhancer Browser—a database of tissue-specific human enhancers
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| Search for information on experimentally validated human noncoding fragments with gene enhancer activity as assessed in transgenic mice.
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Wise2 -- Intelligent algorithms for DNA searches
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| Compare a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
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YIDB -- The Yeast Intron DataBase
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| Search for information about all introns encoded in the nuclear and mitochondrial genomes of the yeast Saccharomyces cerevisiae. |
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Yeast Deletion Project and Proteomics of Mitochondria Database
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| Search for data from the Yeast Deletion, Mitochondrial Proteomics, and Yeast Expression Projects.
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nuScore -- a web-interface for nucleosome positioning predictions
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| Deformation energy and nucleosome-positioning score calculator.
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spliceNest -- Visualizing Splicing of Genes from EST Data
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| Search for computationally predicted human gene structure and splice variants derived from human mRNAs and ETS.
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