基因预测与结构注释
编码基因预测;重复序列注释;Non-coding RNA基因注释;Micro RNA基因注释;tRNA基因注释;假基因(Pseudogene)注释等.
http://fhqdddddd.blog.163.com/blog/static/186991542009111410469680/FgeneSH
Genebuilder
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 On
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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