ORFs, Splicing & Coding
Finding ORFs and predicting coding regions
The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database.
http://www.ncbi.nlm.nih.gov/gorf/gorf.html
This server provides access to the program Genscan for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms. This server can accept sequences up to 1 million base pairs (1 Mbp) in length.
http://genes.mit.edu/GENSCAN.html
Open Reading Frame Retrieval. ORFer is a Java Application that can read the GenBank XML sequence format. Protein sequences can be requested by GI identifier or accession number. The open reading frame corresponding to the protein sequences is extracted from the XML and displayed. ORFer has a database interface that allows for storing the retrieved sequences in a local SQL database. Currently supported: MySQL, Oracle and Micosoft Access.
http://www.proteinstrukturfabrik.de/orfer/
Online ORF analysis giving detailed report.
http://cbcsrv.watson.ibm.com/Tgi.html
The NetStart server produces neural network predictions of translation start in vertebrate and Arabidopsis thaliana nucleotide sequences.
http://www.cbs.dtu.dk/services/NetStart/
Identifies potential exons in human genes
http://www.ebi.ac.uk/asd-srv//splice-prediction/web/wrapper.cgi
Identifies and scores alternative Open Reading Frames (ORF) and translates them into peptides.
http://www.ebi.ac.uk/asd-srv/wb.cgi?method=9
Projector is a program for the comparative, homology based prediction of protein coding genes in mouse and human DNA. Projector takes the known genes of one DNA sequence and predicts the corresponding genes in an evolutionarily related DNA sequence.
http://www.sanger.ac.uk/Software/analysis/projector/
Protea is a software devoted to protein-coding sequences identification. The input is a set of DNA sequences that need not to be aligned. The method takes advantage of the specific substitution pattern of coding sequences together with the consistency of reading frames.
http://bioinfo.lifl.fr/protea/index.php
Gene identification in novel eukaryotic genomes by self-training algorithm
http://opal.biology.gatech.edu/GeneMark/eukhmm.cgi
HMM-based gene structure prediction (multiple genes, both chains)
http://linux1.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind
Splicing, alternative splicing & introns
Ecgene is novel gene prediction program that combined genome-based EST clustering and transcript assembly procedures in a coherent fashion andprovides a genome annotaion for alternative splicing.
http://genome.ewha.ac.kr/ECgene/
Splice Signal Analysis - main page at EBI
http://www.ebi.ac.uk/asd-srv/wb.cgi
Identifies binding sites for splice factors in RNA sequences
http://www.ebi.ac.uk/asd-srv/wb.cgi?method=8
Computes scores at Donor and Acceptor site; identifies Branch Point (BP) and Polypyrimidine Tract (PPT) sites in an intronic sequence.
http://www.ebi.ac.uk/asd-srv/wb.cgi?method=6
A wrapper for Intron Analysis, Regulatory sequences, Exon Finder, Splicing Rainbow, and Blast analysis
http://www.ebi.ac.uk/asd-srv/wb.cgi?method=7
Compares a protein sequence or a protein profile HMM to a DNA sequence, allowing for introns and frameshifting errors. The software can also be downloaded.
http://www.ebi.ac.uk/Wise2/
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.
http://genes.mit.edu/genomescan.html
TassDB stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. Currently, 114,554 tandem splice sites of eight species are contained in the database, 5,209 of which have EST/mRNA evidence for alternative splicing.
http://helios.informatik.uni-freiburg.de/TassDB/
This web interface provides a tool to predict the effects of sequence changes that alter mRNA splicing in human diseases. We designed the system to evaluate changes in splice site strength based on information theory-based models of donor and acceptor splice sites.
https://splice.uwo.ca/
Group II introns are a novel class of RNAs best known for their self-splicing reaction. Under certain in vitro conditions, the introns can excise themselves from precursor mRNAs and ligate together their flanking exons, without the aid of protein.
http://www.fp.ucalgary.ca/group2introns/
The AStalavista web server extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates.
http://genome.imim.es/astalavista/
A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes.
http://cbcb.umd.edu/software/GeneSplicer/
Intronerator - a collection of tools for exploring the molecular biology and genomics of C. elegans with a special emphasis on alternative splicing.
http://hgwdev-hiram.cse.ucsc.edu/IntronWS120/index.html
The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.
http://www.cbs.dtu.dk/services/NetGene2/
Several examples of intronic and exonic cis-elements that are important for correct splice-site identification and are distinct from the classical splicing signals have been described. These elements can act both by stimulating (enhancers) or by repressing (silencers) splicing, and they seem to be especially relevant for regulating alternative splicing. Exonic splicing enhancers (ESEs), in particular, appear to be very prevalent, and may be present in most, if not all exons, including constitutive ones
http://rulai.cshl.edu/cgi-bin/tools/ESE3/esefinder.cgi?process=home
The NetPlantGene server is a service producing neural network predictions of splice sites in Arabidopsis thaliana DNA.
http://www.cbs.dtu.dk/services/NetPGene/
ASPic (Alternative Splicing Prediction) is a web-based tool to detect the exon-intron structure of a gene by comparing its genomic sequence to the related cluster of ESTs.
http://t.caspur.it/ASPIC/
Intron & exon databases
List of Gene structure, introns and exons, splice sites Databses at Nucleic Acid Research.
http://www.oxfordjournals.org/nar/database/subcat/1/3
Hollywood exon annotation database at MIT, a website for querying a relational database of constitutive and alternative human exons, by using biological and descriptive features.
http://hollywood.mit.edu/Logo/index.html
The ExIntTM database is a relation database on the world-wide-web (WWW) containing such information derived from GenBank. Hence, the availability of whole-genome sequences and search engines provides a magnificent laboratory for the investigation of genome evolution in eukaryota. The data and the database help to identify common evolutionary patterns in higher eukaryotic genes for the study of intron loss/gain, sliding, splicing, retroposition, recombination, intron/exon duplication, etc.
http://sege.ntu.edu.sg/wester/exint/
Human-transcriptome DataBase of Alternative Splicing
http://jbirc.jbic.or.jp/h-dbas/index.jsp
DBTSS is a database of transcriptional start sites, based on our unique collection of precise, experimentally-determined 5'-end sequences of full-length cDNAs.
http://dbtss.hgc.jp/
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.
http://bioinformatics.ucla.edu/ASAP2/
HS3D (Homo Sapiens Splice Sites Dataset) is a data set of Homo Sapiens Exon, Intron and Splice regions extracted from GenBank
http://www.sci.unisannio.it/docenti/rampone/
his site contains information about the spliceosomal introns of the yeast Saccharomyces cerevisiae.
http://www.soe.ucsc.edu/research/compbio/yeast_introns.html
YIDB: the Yeast Intron DataBase
http://www-db.embl-heidelberg.de/jss/servlet/de.embl.bk.wwwTools.GroupLeftEMBL/ExternalInfo/seraphin/yidb.html
An exhaustive database of protein-coding intron-containing genes
http://hsc.utoledo.edu/bioinfo/eid/