Intron/exon structure prediction
From MyBio
Users might find Gene Identification tools page useful, and perhaps ORF prediction tools page. Note: ORF stands for Open Reading Frame.
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[edit] Intron - Quick Links
[edit] Intron/exon structure prediction - Web Resources
GeneSplicer Fast flexible system for detecting splice sites in the genomic DNA of various eukaryotes. A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and rice. Training data sets for
GenomeScan This server provides access to the program GenomeScan for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms..
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Exon Locator and Extractor for Resequencing Maps cDNA to genomic sequence and designs primers for amplification and sequencing of exons and other targets. ELXR (Exon Locator and Extractor for Resequencing) was developed to accomplish the steps of exon identification and primer design in a fraction of the time consumed by manual methods. ELXR and ELXRdb, a database of pre-computed primer pairs for all human, mouse and rat RefSeq mRNA sequences mRNA are at http://elxr.swmed.edu. ELXR has been integrated into the high-throughput SNP sequencing pipeline in a NHLBI Program for Genomic Applications at UT Southwestern (http://pga.swmed.edu).
Intronerator Web-based tools for exploring RNA splicing and gene structure in Caenorhabditis elegans.
ExInt Exon Intron Database of Eukaryotic Organisms. The ExInt database incorporates information on exon-intron structure of eukaryotic genes. ExInt accumulates and describes following important characters of the eukaryotic genes: the phases and positions of introns and the exon size and positions of introns for all proteins in GenBank. (The phases of introns, a very conserved evolutionary character refers to the location of introns relative to the three nucleotide positions in triplet codon.) ExInt data is accessible through a retrieval system, which has pointers to NCBI GenBank. The database can be searched by LOCUS name, NID, Accession number or length of the protein. The database is of potential use for molecular biologists in general and for researchers who are interested in gene evolution. There is also a BLAST service against Exint.
SpliceNest Visualizing Splicing of Genes from EST Data.
NetGene2 Splice site prediction, trained on C.elegans and A.thaliana (used to be called NetPlantGene2).
ESEfinder
Web resource to identify exonic splicing enhancers. Some point mutations can have severe effects on the structure of the encoded protein, for example when they inactivate an exonic splicing enhancer (ESE), thereby resulting in exon skipping. ESEs also appear to be especially important in exons that normally undergo alternative splicing. Different classes of ESE consensus motifs have been described, but they are not always easily identified. ESEfinder is a web-based resource that facilitates rapid analysis of exon sequences to identify putative ESEs responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.
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SpliceDB Canonical and non-canonical mammalian splice sites.
ISIS Intron Sequence and Information database. First multiple organism nuclear intron database. This database is searchable by many different criteria including taxanomic searches and searches using common elements contained within introns. Database will facilitate a greater understanding of the role of introns in eukaryote biology.
NetPlantGene CBS. CBS Prediction Servers. NetPlantGene NetPlantGene Server. The NetPlantGene server is a service producing neural network predictions of splice sites in Arabidopsis thaliana DNA. Instructions. Output format. Abstract. Mail Server. ...
Homo Sapiens Splice Sites Dataset
HS3D. HS3D (Homo Sapiens Splice Sites Dataset) is a data set of Homo Sapiens Exon, Intron and Splice regions extracted from GenBank Rel.123. The aim of this data set is to give standardized material to train and to assess the prediction accuracy of computational approaches for gene identification and characterization. From the complete GenBank (Primate Sequences Division) Rel.123 (162,557 entries), entries of Human Nuclear DNA including Complete CDS and more than one Exon have been selected, and 4523 exons and 3802 introns have been extracted from these entries.Details about extracted exons and introns are reported (Locus, number, Start and End position in the entry, sequence, length, G C content, presence of not AGCT data (nucleotide scan check).Statistics are also reported (overall nucleotides, average G C content, nucleotide scan check results, number of not GT starting / AG ending introns, minimum / maximum / average length, length standard deviation).
Mobile group II introns Supported by: - Canadian Institute of Health Research (CIHR). Alberta Heritage Foundation for Medical Researh. (AHFMR). Welcome to the Zimmerly Lab Web Site for Mobile group II introns Update News: Last updated January 25, 2004. Update ...
Ares Lab Yeast Intron db This searchable database contains information about the location, structure, and function of spliceosomal introns in the nuclear genome of Saccharomyces cerevisiae. Searches produce reports for each intron satisfying the search criteria, showing key information, including a short gene description with links to the Saccharomyces Genome Database, estimated transcription rate, special features of the intron, literature or EST verification links, intron size, splice sites and branchpoint sequences and complete sequences of the intron and flanking exons, as well as the sequence generated by splicing. Expression measurements that profile the impact of mutations on the splicing of each intron are also included in the reports.
YIDB
Yeast nuclear and mitochondrial intron sequences. The Yeast Intron DataBase (YIDB) contains currently available information about all introns encoded in the nuclear and mitochondrial genomes of the yeast Saccharomyces cerevisiae. Introns are divided according to their mechanisms of excision: group I and group II introns, pre-mRNA introns, tRNA introns and the HAC1 intron. Information about the host genome, the type of RNA in which they are inserted and their primary structure are provided together with references. For nuclear pre-mRNA introns transcription frequencies have also been included.
Exon-Intron Database (EID) Protein-coding, intron-containing genes - an exhaustive database of protein-coding intron-containing genes. To aid studies of molecular evolution and to assist in gene prediction research, we have constructed an Exon-Intron Database (EID) ...
ASPic (Alternative Splicing Prediction)
Web-based tool detects the exon-intron structure of a gene by comparing its genomic sequence to the related cluster of ESTs, predicts constitutive and alternative splice sites using a combined analysis of all EST alignments.
Augustus: job submission
Predicts genes in eukaryotic genomic sequences using hints compounded from EST and protein databases, able to predict 89% of the exons in human chromosome 22 correctly. Trained to predict genes in human, fruit fly, Arabidopsis and many others.
EDAS: EST-Derived Alternative Splicing Database
Database of alternatively spliced human genes, contains data on alignment of proteins, mRNAs, and EST, information on all exons and introns observed, as well as elementary alternatives formed from them.
