第十章利用核酸序列的预测方法 页码,7/16 简单实例来标定了能得到的程序,结果无一能正确预测出多于一半的外显子);(4)大多 复合算法都明显对测序错误十分敏感( Burst和 Gui go,1996);以及(5)象交替剪接、重 叠基因和启动子结构这样的基因语法结构仍超出当前程序的处理能力。 既然这些程序中没有一个十全十美,它们都覆盖了一些不同算法,都在迅速进步,因此强烈 建议分析每个序列时采用3到4个不同程序,并仔细对比其结果。如果某个工具会经常用到, 就值得用大量已知结果的序列对其进行测试,以便对算法适用性有所了解。 表10.1因特网上的编码蛋白基因识别工具 Servi ce Organi sm(s) EcoParse Krogh et al. (1994) Escherichi a coli e-maI I: ecopa FGENEH/D/N/Y/A Sol ovyev and Mammal i an, Drosophila e-mail:ana/」 al amoy (1997) CDSB (1997) nematode, yeast, pl ant, and bacteri a httpdefra GeneI d Gui go et al.(1992)Vertebrate e-mai l: genei GeneMark Borodovsky and Many i ndi vi dual speci es e-mai I genen Mcl ni nch(1993) http://intrc GeneParser Snyder and Stormo Human http://beag (1995) Genie Kul p et al.(1996)Human http://www-f GenLang Dong and Searls Di cotyl edons, Drosophila,vertebrates e-mai l: gen/a (1994) http://cbi/ GENSCAN Burge and Karl in Vertebrate, Caenorhabdi tis, mai ze, Arabidopsis e-mai l: genso (1997) http://gnon EnvI ew Mi I anesi et al. Human, mouse, Di ptera http://www.i (1993) GRAI L/GAP/ Xu et al.(1994) Human e-mai l: grail XGRAIL http://avalc MZEF Zhang(1997) Human, mouse, Arabi dopsis, fi ssi on yeast http://www.c Procrustes Gel fand et al http://www-f (1996) Predi cted ger nes/exons Gn. Ex Type S. Begi n.. End. Len Fr Ph I/Ac Do/T CodRg P....Tscr file://E:wcb生物信息学(中译本)\第十章利用核酸序列的预测方法.htm2005-1-18Ͼㅔऩᅲ՟ᴹᷛᅮњ㛑ᕫࠄⱘ⿟ᑣˈ㒧ᵰ᮴ϔ㛑ℷ⹂乘⌟ߎ໮Ѣϔञⱘ໪ᰒᄤ˅˗˄˅໻໮ ໡ড়ㅫ⊩䛑ᯢᰒᇍ⌟ᑣ䫭䇃कߚᬣᛳ˄Burset੠Guigóˈ1996˅˗ҹঞ˄˅䈵Ѹ᳓࠾᥹ǃ䞡 ঴෎಴੠ਃࡼᄤ㒧ᵘ䖭ḋⱘ෎಴䇁⊩㒧ᵘҡ䍙ߎᔧࠡ⿟ᑣⱘ໘⧚㛑࡯DŽ ᮶✊䖭ѯ⿟ᑣЁ≵᳝ϔϾकܼक㕢ˈᅗӀ䛑㽚Ⲫњϔѯϡৠㅫ⊩ˈ䛑೼䖙䗳䖯ℹˈ಴ℸᔎ⚜ ᓎ䆂ߚᵤ↣Ͼᑣ߫ᯊ䞛⫼ࠄϾϡৠ⿟ᑣˈᑊҨ㒚ᇍ↨݊㒧ᵰDŽབᵰᶤϾᎹ݋Ӯ㒣ᐌ⫼ࠄˈ ህؐᕫ⫼໻䞣Ꮖⶹ㒧ᵰⱘᑣ߫ᇍ݊䖯㸠⌟䆩ˈҹ֓ᇍㅫ⊩䗖⫼ᗻ᳝᠔њ㾷DŽ 㸼10.1಴⡍㔥Ϟⱘ㓪ⷕ㲟ⱑ෎಴䆚߿Ꮉ݋ Predicted genes/exons: Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr.. Service Ref. Organism(s) EcoParse Krogh et al.(1994) Escherichia coli e-mail:ecoparse@cse.ucsc.edu FGENEH/D/N/Y/A Solovyev and Salamov(1997) Mammalian,Drosophila. e-mail:analysis@theory.bchs.uh.edu CDSB (1997) nematode,yeast,plant,and bacteria http://defrag.bcm.tmc.edu:9503/ltp.html GeneID Guigo et al.(1992) Vertebrate e-mail:geneid@darwin.bu.edu GeneMark Borodovsky and Mclninch(1993) Many individual species e-mail:genemark@ford.gatech.edu http://intron.biology.gatech.edu/~genmark GeneParser Snyder and Stormo (1995) Human http://beagle.colorado.edu/~eesnyder/GeneParser.html Genie Kulp et al.(1996) Human http://www-hgc.lbl.gov/inf/genie.html GenLang Dong and Searls (1994) Dicotyledons,Drosophila,vertebrates e-mail:genlang@cbil.humgen.upenn.edu http://cbil.humgen.upenn.edu/~sdong/genlang_home.html GENSCAN Burge and Karlin (1997) Vertebrate,Caenorhabditis,maize,Arabidopsis e-mail:genscan@gnomic.stanford.edu http://gnomic.stanford.edu/~chris/GENSCANW.html GenView Milanesi et al. (1993) Human,mouse,Diptera http://www.itba.mi.cnr.it/webgene GRAIL/GAP/ Xu et al.(1994) Human e-mail:grail@ornl.gov XGRAIL http://avalon.epm.ornl.gov/gallery.html MZEF Zhang(1997) Human,mouse,Arabidopsis,fission yeast http://www.cshl.org/geneginder Procrustes Gelfand et al. (1996) Any http://www-hto.usc.edu/software/procrustes ㄀कゴ߽⫼Ḍ䝌ᑣ߫ⱘ乘⌟ᮍ⊩ 义ⷕˈ7/16 file://E:\wcb\⫳⠽ֵᙃᄺ˄Ё䆥ᴀ˅?㄀कゴ߽⫼Ḍ䝌ᑣ߫ⱘ乘⌟ᮍ⊩.htm 2005-1-18 Click to buy NOW! PDF-XCHANGE www.docu-track.com Click to buy NOW! PDF-XCHANGE www.docu-track.com