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/
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
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/
Human-transcriptome DataBase of Alternative Splicing
http://jbirc.jbic.or.jp/h-dbas/index.jsp
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/
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