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AAT http://genome.cs.mtu.edu/aat.html    基因组序列基因预测
BGF http://tlife.fudan.edu.cn/bgf   真核生物基因预测*****
GeneFinder http://cgap.nci.nih.gov/Genes/GeneFinder   基因预测
Geneid http://genome.imim.es/software/geneid/index.html 基因预测
Genlang hhtp://arete.ibb.waw.pl/PL/html/gene_lang.html        基因预测序列分析
GENSCAN http://genes.mit.edu/GENSCAN.html      真核生物基因预测   *****

GENEWISE
Glimmer http://www.cbcb.umd.edu/software/glimmer 原核生物基因预测
AUGUSTUS:http://augustus.gobics.de/ 真核基因

Genemark: http://exon.biology.gatech.edu/

GlimmerM http://www.tigr.org/tdb/glimmerM/glmr_form.thml 真核生物基因预测*****
GrailEXP http://grail.lsd.ornl.gov/grailexp 外显子基因预测*****
Twinscan http://www.bioinformatics.ubc.ca/resources/tools/twinscan 真核生物基因预测*****

EVM http://evidencemodeler.sourceforge.net/

GenomeThreader http://www.genomethreader.org/ 植物基因预测

1 基于相似性的基因预测方法： sim4 ，Spidey ，Genewise， TwinScan

2 基于统计学模型的预测方法物猜测软件：Glimmer GenScan ，Fgenesh、BGF

剪切位点

Software tools for prediction of splicing sites

Program	Author, WWW site	Training sets	Refs.
HSPL	Victor Solovyev, http://genomic.sanger.ac.uk/gf/gf.shtml	Human	[792]
NNSplice	Martin Reese, http://www.fruitfly.org/seq_tools/splice.html	Human, Drosophila	[696]
SpliceView	Igor Rogozin, Luciano Milanesi http://www.itba.mi.cnr.it/webgene/	Human, yeast, Drosophila, Arabidopsis	[710]
NetGene2	S?ren Brunak, http://www.cbs.dtu.dk/services	Human, C. elegans, Arabidopsis	[123]
GeneSplicer	Steven Salzberg, http://www.tigr.org/softlab	Human, Arabidopsis	[672]
SpliceProximalCheck	Thangavel Thanaraj http://industry.ebi.ac.uk/~thanaraj/MZEF-SPC.html	Human	[838]

SplicePort http://spliceport.cs.umd.edu/

GeneSplicer http://cbcb.umd.edu/software/GeneSplicer/

JIGSAW http://cbcb.umd.edu/software/jigsaw/ JIGSAW is a program designed to use the output from gene finders, splice site prediction programs and sequence alignments to predict gene models Margin-based Prediction of Polymorphic Regions -mPPR

http://www.fml.tuebingen.mpg.de/raetsch/suppl/mppr

Accurate Splice Site Detection (Supplementary Material) http://www.fml.tuebingen.mpg.de/raetsch/suppl/splice

Tutorial http://svmcompbio.tuebingen.mpg.de/

EST2genome

http://www.umanitoba.ca/afs/plant_science/psgendb/doc/doc/emboss/programs/html/est2genome.html
功能注释

预测的基因进行功能(Gene On

tology,调控Motif,Pathway等)注释

CAZY: www.cazy.org

KEGG 由6个独立数据库基因、通路、配体化学反映、序列相似、基因表达、蛋白质相互关系 : www.genome.jp/kegg

NOG 对同源基因的功能注释: http://eggnog.embl.de/

Gene Ontology 基因功能分类体系: www.geneontology.org

JGI annotation （注释）http://www.jgi.doe.gov/ :微生物细菌

InterProScan GO(注释软件） http://www.ebi.ac.uk/Tools/InterProScan/

http://www.geneontology.org/GO.annotation.interproscan.shtml

http://www.cbs.dtu.dk/services/SignalP/

GBrowse:http://gmod.org/wiki/Downloads 基因表达分析 GBrowse

RiceGAAS: Rice Genome Automated Annotation System ： http://ricegaas.dna.affrc.go.jp/
比较基因组和分子进化分析:
如快速进化(rapid evolution)分析,共线性分析(Synteny Block),基因家族分析等;

常用的进化树分析软件:

MEGA:http://www.megasoftware.net/

预测拓扑结构:预测下蛋白的跨膜结构

http://genome.cbs.dtu.dk/services/TMHMM-1.0/
http://www.ch.embnet.org/software/TMPRED_form.html

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