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常用基因预测软件:Gene finders and other sequence analysis programs list  

2011-08-03 10:30:34|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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Glimmer is a system that uses Interpolated Markov Models (IMMs) to identify coding regions in microbial DNA. IMMs are a generalization of Markov models that allow great flexibility in the choice of the "context"; i.e., how many previous bases to use in predicting the next base. Glimmer has been tested on the complete genomes of H. influenzae, E. coli, H. pylori, M. genitalium, and other genomes, and results to date have proven it to be highly accurate. Glimmer was the principal gene finder for the genomes of B. burgdorferi , T. pallidum, C. trachomatis, C. pneumoniae, D. radiodurans, T. maritima, and others. The complete system, including source code, is available from this site.  A version of the system built for the malaria parasite, GlimmerM, is also available.
GeneFinding.org is a page with links to most of the latest eukaryotic gene finders.   It has much better links and is more up to date than most of the links below.
GENSCAN is a program designed to predict complete gene structures, including exons, introns, promoter and poly-adenylation signals, in genomic sequences. It differs from the majority of existing gene finding algorithms in that it allows for partial genes as well as complete genes and for the occurrence of multiple genes in a single sequence, on either or both DNA strands. Program versions suitable for vertebrate, nematode (experimental), maize and Arabidopsis sequences are currently available. The vertebrate version also works fairly well for Drosophila sequences. Sequences can be submitted on a web-based form at this site. The GENSCAN Web site is at Stanford University.
GeneMark is a system for finding genes in bacterial DNA sequences. The algorithm is based on non-homogeneous 5th-order Markov chains, and it was used to locate the genes in the complete genomes of H. influenzae, M. genitalium, and several other complete genomes. The site includes documentation and a Web interface to which sequences can be submitted. This system is at the Georgia Institute of Technology in Atlanta, GA.
NetPlantGene is at the Technical University of Denmark. The NetPlantGene Web server uses neural networks to predict splice sites in Arabidopsis thaliana DNA. This site also contains programs for other sequence analysis problems as well, such as the recognition of signal peptides. NetPlantGene is to be replaced with NetGene2.
Repeat Pattern Toolkit (RPT) consists of tools for analyzing repetitive sequences in a genome. RPT takes as input a single sequence in GenBank format, and attempts to find both coding (possible gene duplications, pseudogenes, homologous genes) and non-coding repeats. RPT locates all repeats using a fast Senstive Search Tool (SST). These repeats are evaluated for statistical significance utilizing a sensitive All-PAM search, and their evolutionary distance is estimated. The repeats are classified into families of similar sequences. The classification output is tabulated using perl scripts and plotted using gnuplot. RPT is at the Institute for Biomedical Computing at Washington University in St. Louis.
SplicePredictor is a program designed to predict donor and acceptor splice sites in maize and Arabidopsis sequences. Sequences can be submitted on a web-based form at this site. The system is at Stanford University.
TESS (Transcription Element Search Software) is a set of software routines for locating and displaying transcription factor binding sites in DNA sequence. TESS uses the Transfac database as its store of transcription factors and their binding sites. This page is at the University of Pennsylvania's Computational Biology and Informatics Laboratory.
Genotator, a workbench for automated sequence annotation, provides a flexible, transparent system for automatically running a series of sequence analysis programs on genetic sequences. It also has a graphical display that allows users to view all of the automatically-generated annotations and add their own. Genotator's display allows annotated sequences to be examined at multiple levels of detail, from an overview of the entire sequence down to individual bases. By displaying the aligned output of multiple types of sequence analysis, Genotator provides an intuitive way to identify the significant regions (for example, probable exons) in a sequence. Genotator was developed by Nomi Harris at Lawrence Berkely National Laboratory.
WebGene (GenView, ORFGene, SpliceView) is Web interface for several coding region recognition programs, including:
GenView: a system for protein-coding gene prediction
ORFGene: gene structure prediction using information on homologous protein sequences
SpliceView: prediction of splicing signals
HCpolya: a hamming Clustering Method for Poly-A prediction in eukaryotic genes
This page is at the Instituto Tecnologie Biomediche Avanzate in Italy.
The Staden Package contains a wealth of useful programs for sequence assembly, DNA sequence comparison and analysis, protein sequence analysis, and sequencing project quality control. The site is mirrored in several locations around the world. 

more information links to:http://www.cbcb.umd.edu/~salzberg/appendixa.html

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