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A??á ü,X ? ′A??áu/?c?????¤oú/?,X>y&?NX#?_Vè FGENEH/D/N/A/?c ,X H/D/N/ASPL?úè Solovyev ` Salamovè 1997??!8êè Brunak1? 1991?¤o(à0?,X>y &?NX#/?c NetGene???0′??><?èú>y&?DμCaí?{4ê-?,XA?4§ üCK9? 5?A￥CK?!&? íb,ó *ó(=èVpE@)CK?&??-1èJè"uYY ?$'? 5'M25?A￥ ,XA±è Kozak??í ? Kozakè 1996? ?1 ü??D???n!CK??-?$? s *ó(=?8"uY>yE?/?è ü? KùA?R!7.B,XCK??-?$?\ ?L??E-/???G?è+b?NN ??4?$,X, üè |$ n!<QY*üèáB5 ü,ó *ó(=CKGK0*ü?í s *ó(=èGK 2a'4§ ü&?,X ?M4n !?E-?,?,X ?1+?t/?c¤o?·?è?? GelFand? 1995?4DE?? 4?!6μ ? ?7N8?ê `5?A￥4?!6μ ?,?T ?"uY ? ′CK?μ ?FwG??UèE-oμ ?36?}?ú ? ′ ,X8× è?_$ ??? Kondrakhin1? 1994?è Wahle ` Keller? 1996?è Dalphin1? 1997?è 1 ? Solovyev ` Salamov? 1997?1í!8,XLE?? á ü,X ? ′Aá"?úd 1?·Au1kEY} ? ′A??/?c?U?)úA?? ? ′,Xú/?(MU##_Vè )(àA??>y! &?èê5ù ?A??á#] ?μ ?,X4ê-? ,X??í??!¨?AèVp?t>y!&?ú?!?4ê-? Lh ?èFwW6?}?#ê ü?E??R4ê-? è5à ü o?E?RM24ê-? ?E-Aèa4D ü5×<%Yn (MU,XH'?7è?6?:+¤P?NX#,X2?z?_Vè 60á,X 50bp1?KSz,Xê$ ü1!,X GRAIL+ $F?êáu/?c?>F+$?è ütT?t1T ),X>y `?FEeúd a6?ó>? #?9? Einstein1è 1992?? á ü,X ? ′e?/?ce2?μ ?c?J04ê-? úd?Yê30 à$dc?e2???' aèí ,ìh'ú?DEˉ> ìêè1.Bnê$J4-?aTYDB,?T ???7è,X?o ?6?,X ? ′4§X?á?¤P?2?z `S*ü,X?y||E-o/?cá? ￥),XG??U|o? )? ü6?kA??E- ,Xá ü1k"??>< 10.1?è7?? ü?o???Wà6?4-?Gb ? ′4§X,X ?oQ???? ò 10.3/Z*ü GENSCAN?FB;G?ác? a?úd?2O.?GLíGBGL" üGJ ? ′ ? HSENO3×#?t ? X56832?,X4§p? ü Fickett ` Guigó? 1996?[)6?R*üJW?o/?cúdE-t ? ′,X4§p?Zí!¨è E-G? GenBankíE-t ? ′,X"??·? CDS join (1579..1663, 2540..2635, 2796..2854, 3016..3085, 3455..3588, 4820..5042, 5153..5350, 5688..5889, 6318..6426, 6576..6634, 6723..6792) >< 10.2ú4§p?è?bKùA?,X??? E-o/?c? üE-??TNZ 3,X1?·?,X?UL$? üb???á ü,X1k"?,?! ?E?*ü ?D(=/?×??Y,X/?c?L8Z GENSCAN? üEg9c?ù ?? ? ′ê5ùF?ú ? ′êè NX#,Xê$? ?M4èNX#,X ? ′4§Xá?nZ×??+b?á`<#ù.,X s ′èNX #2?z ?6?!¨ s?B5,X"k?è?Jí? ￥)?,X ? ′?? Burset ` Guigóè 1996è*ü,R9 NI-?è 6/161 0′y*ü GLc?,XNX#?"? 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1 0′y*ü GLc?,XNX#?"? .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om t1T )r_9?nZ6?k,X/?cè4§p′?6?!7.BNX#??b? ,Xê$?×???? á ü1k"?F?aí#cJíA? ú#ó? Burset ` Guigóè 1996?×1 ???B5xó>y?G? ′ ? ′ ` |$4§XE- ,X ? ′Aá"?4§X?CY?'!/?c,X?)ú6?o? ?' E-o/?c"uY?t < 5bèWàF??Z,aZ?oá à1k"?èF? üE?EóEˉ!9è ′!8&? ?A?úd!￡tc?êG?*ütá à/?cèJ¨4?í!¨J4§p?Vp¤t1K?4￡ *üè k*ü?G￡?-14§p,Xc?íJEˉ> #A?è1?í1k"?E?*ü?YZ?·? >< 10.1 ′(M5%T,X4ê-?<?,Q ? ′A??1K 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 NI-?è 7/161 0′y*ü GLc?,XNX#?"? 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1 0′y*ü GLc?,XNX#?"? .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om 1.01 Init + 1579 1663 85 0 1 114 54 131 0.741 13.24 1.02 Intr + 2540 2635 96 0 0 1 100 134 0.698 6.38 1.03 Intr + 3455 3588 134 0 2 101 81 136 0.999 15.07 1.04 Intr + 4820 5042 223 1 1 85 56 432 0.998 37.93 1.05 Intr + 5153 5350 198 0 0 73 81 371 0.999 34.74 1.06 Intr + 5688 5889 202 1 1 53 69 378 0.979 31.27 1.07 Intr + 6318 6426 109 0 1 62 80 20 0.843 0.61 1.08 Intr + 6576 6634 59 2 2 105 77 51 0.888 3.87 1.09 Term + 6723 6792 70 0 1 63 54 98 0.785 1.61 1.10 PlyA + 6853 6858 6 1.05 Predicted peptide sequence(s): >gi|GENSCAN_predicted_peptide_1|391_aa MAMQKIFAREILDSRGNPTVEVDLHTAKGRFRAAVPSGASTGIYEALELRDGDKGRYLGK AKFGANAILGVSLAVCKAGAAEKGVPLYRHIADLAGNPDLILPVPAFNVINGGSHAGNKL AMQEFMILPVGASSFKEAMRIGAEVYHHLKGVIKAKYGKDATNVGDEGGFAPNILENNEA LELLKTAIQAAGYPDKVVIGMDVAASEFYRNGKYDLDFKSPDDPARHITGEKLGELYKSF IKNYPVVSIEDPFDQDDWATWTSFLSGVNIQIVGDDLTVTNPKRIAQAVEKKACNCLLLK VNQIGSVTESIQACKLAQSNGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSER LAKYNQLMRIEEALGDKAIFAGRKFRNPKAK Column Description Gn.Ex gene number, exon number (for reference) Type Init = Initial exonIntr = Internal exon Term = Terminal exonSngl = Single exon gene Prom = PromoterPlyA poly A signal NI-?è 8/161 0′y*ü GLc?,XNX#?"? 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1 0′y*ü GLc?,XNX#?"? .htm Click to buy NOW! 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PDF XCHANGE ww w.d ocu track.c om S DNA strand (* = input strand; = opposite strand) Begin beginning of exon or signal (numbered on input strand) End end point of exon or signal (numbered on input strand) Len length of exon or signal (bp) Fr reading frame (a codon ending at x is in frame f x modulo 3) Ph net phase of exon (exon length modulo 3) I/Ac initiation signal or acceptor splice site score (x 10) Do/T donor splice site or termination signal score (x 10) CodRq coding region score (x 10) P probability of exon (sum over all parses containing exon) Tscr exon score (depends on length, B/Ac, Do/T and CodRg scores) ò 10.3 GENSCANúd _,XEg?4§pèAo??!7[? >< 10.2í!¨NX#4§p ` ? ′"??· Predicted Exons Annotated Exons 1579 1663 1579 1663 2540 2635 2540 2635 2796 2854 3016 3085 3455 3588 3455 3588 4820 5042 4820 5042 5153 5350 5153 5350 5688 5889 5688 5889 6318 6426 6318 6426 6576 6634 6576 6634 6723 6792 6723 6792 NI-?è 9/161 0′y*ü GLc?,XNX#?"? 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1 0′y*ü GLc?,XNX#?"? .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om e? tRNA ? ′ í tRNA ? ′,XA???U?bA??4ê-?<?,Q,X ? ′F?ú+b pol |$4§X1T )1 ? tRNA` 4{4§X,X±\?? ü tRNAscan SE? Lowe ` Eddyè 1997?è4§ üZ?t?ó/?cè ?T?· ?Z tRNA ? ′A??,XK?Nl? Lowe ` Eddy ￥)?èúqC*b`4{4§X?1 `±|$ê,X PWM ?#,X tRNAscan? Fichant ` Burksè 1991?,XNX#4§pèaqC*bE@){ êúd,X Pavesi1? 1994?,X1k"?t1 üJ aèCYE? 99á,X,ó tRNA ? ′F?6?>A???9?E-/?#? `,X NX#4§p?><E?ù ?ZCYE? 50á,XL???/?\Q,XEY??1k"?è COVELS? Eddy ` Durbinè 1994? ￥)?6?L8 ??><′"<F?,XJíA??Ht4§p?/?ByF'/?6?A?? 99á ,X,ó tRNA ? ′èJ ü!￡t ? ′4??b?tL?,X?"?? tRNAscan SE,Xáu `ECê  ?k ???0′??><?? ò 10.44-?Z?t_$,XEg?4§p? Sequence tRNA Bounds tRNA Anti Intron Bounds Cove Name tRNA # Begin End Type Codon Begin End Score Your seq 1 2348 2420 Val TAC 0 0 76.52 Your seq 2 2440 2512 Thr TGT 0 0 77.70 Your seq 3 2522 2594 Lys TTT 0 0 84.24 Your seq 4 2627 2698 Gly GCC 0 0 75.46 Your seq 5 2709 2794 Leu TAA 0 0 62.99 Your seq 6 2803 2876 Arg ACG 0 0 71.02 Your seq 7 2900 2973 Pro TGG 0 0 79.67 Your seq 8 2997 3069 Ala TGC 0 0 71.25 Your seq 9 4841 4914 Ile GAT 0 0 84.04 ò 10.4 tRNAscan SEí _,XEg?4§p? _c? SA5SRRè#?t ? L36472è$db Staphylococcus aureus?J tRNA ? ′NX#4§pa DDBJ/EMBL/GenBank,X"??·`<?7è? t9,X)? üá!èBE?*ü \L?k?Q,XT1K?Lc-?G￡ ′(M5%áu6???kè1 ?E?E? ?t )4?+ M66?á?¤oáu,X WWW5%NIèE-/???k1QE@?<Q' V!8è?t*ü ?S*ü ?H+ üE?,X1k"?èk?U?úDB¤x4-?? ú/?c×!8êèE??U^DBE?E? ′(M5%E? ? ??81#] ?Ld/?ítL?Nl?èê5ù ?YA??t/?c ,99? a `]>?,ìh/?c? ü???? #cè?NO ￥a??/??"?è7?|úc?¤x4- ?t/?cèJúY4§pH)ú#ù. ax 4-?4?*ü ?VpY?/?1K4? ü,X'2??èA?5x'??t? ,(à0?Eˉ> ? ￥è ?6? A} ? ?E?,ìí1T )4ê/?A?4?,X105ù6?úE-o/?c4? ü??4?E?*üb?K?rP`xL??U,X?·? ?èE-ú??t\Y?,XEˉ!9?E-/?'2??h ?b+ $F?êê World Wide Web? ?t?,X|?,X ￥)A? ò^'!íE@)A×8V ,X-1A?=abECêè1E?E?Au1kúd ? ′ NI-?è 10/161 0′y*ü GLc?,XNX#?"? 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1 0′y*ü GLc?,XNX#?"? .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om ü(MnT?[,X><E?¤?????A??Yn<?,Q4§ ü!&?,X?"? ü Frech1? 1997?Y4DE?? E@)T?[(M??,?CK9E? qM4!¨ )t ′$4§ üèá,X???n DNATE-/???,X s6?6(2?,X?ó?A?Y? Claverie ` Sauvaget? 1985?è Fondrat ` Kalogeropoulos ? 1994?è Fickett(1996)è Pedersen1? 1996?è1 ? Tronche1? 1997??<Q' ￠ DNAc? NX# ? ′><E???,Xr*ü1K,?!E?"uYè|#E-/?1K? üt9′H?)? Há′ F')ú,X? 1 100′G?ác?úd `JWY?,X ′(M5%C$d??? SERVICE ORGANISM(S) ADDRESS Repeat Analysis CENSOR: annotates repeats in sequence and masks them out Human or rodent e mail:sensor@sharon.lpi.org see also http://www.girmst.org Repbase: repeat collections Human and several other collections ftp ncbi.nlm.nih.gov; reposttory/repbase/REF; also http://www.girinst.org Repeat Masker: annotates repeats in sequence and masks them out Several sub groups of vertebrates http://ftp.genome.washington.edu./index.html XBLAST: tools to mask repeat occurrencts Any ftp ncbi.nlm.nih.gov; pub/jmc Other Topics BCM Search Launcher (interface to multiple analysis tools) Any http://gc.bcm.tmc.edu:8088/search launcher/launcher.html Bibiography for computational gene indentification All http://linkage.rockefeller.edu/wli/gene/list.html Netgene (splice site identification) Human e mail:netgene@cbs.dtu.dk Procrustes (gene delineation by alignment) Any http://www hto.usc.edu/software/procrustes NI-?è 11/161 0′y*ü GLc?,XNX#?"? 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1 0′y*ü GLc?,XNX#?"? .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om 7èA? E-NM10+ SmithKline Beecham Pharmaceuticals?èJ+ National Human Genome Research Institute,X Public Health Service C} HG00981 01A1? ?5×[) Aaronson, J., Eckman, B., Blevins, R. A., Borkowski, J., Imran, S. And Elliston, K. O. (1996). Toward the development of a gene index to the human genome: An assessment of the nature of high throughput EST sequence data. Genome Res. 6, 829 845. Barrick, D., Vilaneuba, K., Childs, J., Kalil, R., Schneider, T. D.,Lawrence, C. E., Gold, L., and Stormo, D. (1994). Quantitative analysis of ribosome bingding sites in E. coli. Nucl. Acids Res. 22, 1287 1295. Bork, P. (196). Go hunting in sequence databases but watch out for the traps. Trends Genet. 12, 425 427. Borodovsky, M., and Mclninch, J. (1993). Genmark: Parallel gene recognition for both DNA strands. Compu. Chem. 17,123 134. Breiman, L., Friedman, J. H., Olshen, R. A., and Stone, C. J. (1984). Classification and Regression Tress (Pacific Grove, CA: Wadsworth and Brooks/Cole). Brunak, S., Engelbrecht, J., and Knudsen, S. (1991). Prediction of humjan mRNA donor and acceptor sites from the DNA sequence. J. Mol. Biol. 220. 49 65. Burge, C., and Karlin, S. (1997). Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78 94. Burset, M., and Guigó, R. (1996). Evaluation of gene structure prediction programs. Genomics 34, 353 367. Claverie, J. M., (1996). Effective large scale sequence similarity searches. Methods Enzymol. 266,212 227. Claverie, J. M., and Sauvaget, I. (1985). Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat shock and glucocorticoild control elements in eukaryotic promoters. Comput. Appl. Biosci. 1, 95 104. Dalphin, M. E., Brown, C. M., Stockwell, P. A., and Tate, W. P. (1997). The translational signal database, TransTerm: More organisms, complete genomes. Nucl. Acids Res. 25, 246 247. Dong, S., and Searls, D. B. (1994). Gene structure prediction by linguistic methods. Genomics 23, 540 551. Doolittle, R. F. (1986). Of URFs and ORFs (Mill Valley. CA: University Science Books). Duret, L., and Bucher, P. (1997). Searching for regulatory elements in human noncoding TRNAscan SE (tRNA gene identification) Any http://genome.wustl.edu/eddy/ NI-?è 12/161 0′y*ü GLc?,XNX#?"? 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1 0′y*ü GLc?,XNX#?"? .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om squences. Curr. Opin. Struct. Biol. 7, 399 406. Eddy, S. R., and Durbin, R. (1994). RNA sequence analysis using covariance models. Nucl. Acids Res. 22, 2079 2088. Einstein, J. R., Mural, R. J., Guan, X., and Uberbacher, E. C. (1992). Computer Based Construction of Gene Models Using the GRAIL Gene Assembly Program. Oak Ridge National Laboratory Report TM 12174 (Oak Ridge, TN ORNL). Fichant, G., and Burks, C. (1991). Identifying potential tRNA genes in genomic DNA sequences. J. Mol. Biol. 220, 659 671. Fickett, J. W. (1996). Coordinate positioning of MEF2 and myogenin binding sites. Gene 172, GC19 GC32. Fickett, J. W., and Guigó, R. (1996). Computational gene identification. In Internet for the Molecular Biologist, S. R. Swindell, R. R. Miller, and G. Myers, Eds. (Washington, DC: Horizon Scientific Press), pp. 73 100. Fickett, J. W., and Hatzigeorgious, A. G. (1997). Eukaryotic promoter recognition. Genome Res. 7, 861 878. Fickett, J. W., and Tung, C. S. (1992). Assessment of protein coding measures. Nucl. Acids Res. 20, 6441 6450. Fondrat, C., and Kalogeropoulos, A. (1994). Approaching th function of new genes by the detection of their potential upstream activation sequences in Saccharomyces cerevisiae: Application to chromosome  . Curr. Genet. 25, 396 406. Frech, K., Quandt, K., and Wemer, T. (1997). Finding protein binding sites in DNA sequences: The next generation. Trends Biochem. Sci. 22, 103 104. Gelfand, M. S. (1995). Prediction of function in DNA sequence analyis. J. Comput. Biol. 2, 87 115. Gelfand, M. S., Mironov, A. A., and Pevzner, P. A. (1996). Gene recognition via spliced alignment. Proc. Natl. Acad. Sci. U.S.A. 93,9061 9066. Gish, W., and States, D. J. (1993). Identification of protein coding regions by database similarity search. Nature Genet. 3, 266 272. Green, P., Lipman, D., Hillier, L., Waterston, R., States, D., and Claverie, J. M. (193). Ancient conserved regions in new gene sequences and the protein databases. Science 259,1711 1716. Guigó, R. (1997). Computational gene identification. J. Mol. Med. 75, 389 393. Guigó, R., Knudsen, S., Drake, N., and Smith, T. (1992). Prediction of gene structure. J. Mol. Biol. 226, 141 157. Hillier, L., Lennon, G., Becker, M., Bonaldo, M. F., Chiapelli, B., Chissoe, S., Dietrich, N., DuBuque, T., Favello, A., Gish, W., Hawkins, M., Hultman, M., Kucaha, T., Lacy, M., Le, M., Le, N., Mardis, F., Moore, B., Morris, M., Parsons, J., Prange, C., Rifkin, L., Rohlfing, T., Schellenberge, K., NI-?è 13/161 0′y*ü GLc?,XNX#?"? 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1 0′y*ü GLc?,XNX#?"? .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Soares, M. B., Tan F., Thierry Meg, J., Trevaskis, E., Underwood, K., Wohldman, P., Waterston, R., Wilson, R., and Marra, M. (1996). Generation and analysis of 280,000 human expressed sequence tags. Genome Res. 6,807 828. Jurka, J., Klonowski, P., Dagman, V., and Pelton, P. (1996). CENSOR&#0;A program for identification and elimination of repetitive elements from DNA sequences. Comput. Chem. 20, 119 122. Knudsen, S., and Brunak, S. (1997). Kissing loops hide premature termination codons in pre mRNA of selenoprotein genes and in genes containing programmed ribosomal frameshifts. RNA 3, 697 701. Kondrakhin, Y., Shamir, V., and Kolchanov, N. (1994). Construction of a generalized consensus matrix for recognition of vertebrate pre mRNA 3' terminal processiong sites. Comput. Appl. Biosci. 10, 597 603. Kozak, M. (1996). Interpreting Cdna SEQUENCES: Some insights from studies on translation. Mamm. Genome 7, 563 574. Krogh, A., Mian, I. S., and Haussler, D. (1994). A hidden Markov model that finds genes in E. coli DNA. Nucl. Acids Res. 11, 4768 4778. Kulp, D., Hausslet, D., Reese, M. G., and Eckman, F, H, (1996). A generalized hidden Markov model for the recognition of human genes in DNA, In Proceedings of the Fourth International Conference on Intelligent Systems in Molecular Biology. D. J. States, P. Agarwal, T. Gaasterland, L. Hunter, and R. Smith, Eds. (Menlo Park, CA: AAA1 Press), pp. 134 142. Lowe, T. M. and Eddy, S. R. (1997). TRNAscan SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl. Acids Res. 25, 955 964. McKeown, M. (1992). Alternative mRNA splicing. Annu. Rev. Cell Biol. 8. 133 155. Milanesi, L., Kolchanov, N. A., Rogozin, I. B., Ischenko, I. V., Kel, A. E., Orlov, Yu. L., Ponomarenko, M. P., and Vezzoni, P. (1993). GenView: A computing tool for protein coding regions prediction in nucleotide sequences. In Proceedings of the Second International Conference on Bioinformatics. Supercomputing and Complex Genome Analysis. H. A. Lim, J. W. Fickett, C. R. Cantor, and R. J. Robbins, Eds. (Singapore: World Scientific Publishing), pp. 573 588. Nilsen, T. W. (1996). A parallel spliceosome. Science 273, 1813. Pavesi, A., Conterio, F., Boichi A., Dieci, G., and Ottonello, S. (1994). Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions. Nucl. Acids Res. 2, 1247 1256. Pedersen, A. G., Baldi, P., Brunak, S. And Chauvin, Y. (1996). NI-?è 14/161 0′y*ü GLc?,XNX#?"? 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1 0′y*ü GLc?,XNX#?"? .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Characterization of prokaryotic and eukaryotic promoters using hidden Markov models. In Fourth International Conference on Intelligent Systems in Molecular Biology. D. J. States, P. Agarwal, T. Gaasterland, L. Hunter, and R. Smith, eds. (Menlo Park, CA: AAA1 Press), pp. 182 191. Robison, K., Gilbert, W. And Church, G. M. (1994). Large Scale Bacterial Gene Discovery by similarity search. Nature Genet. 7, 205 214. Rosenblueth, D. A., Thieffry, D., Huerta, A. M., Salgado, H., and Collado Vides, J. (1996). Syntactic recognition of regulatory regions in Escherichia coli. Comput. Appl. Biosci. 12, 415 422. Senapathy, P., Shapiro, M. B., and Harris, N. L. (1990). Splice Junctions, branch point sites, and exons: Sequence statistics, Identification, and applications to genome project. Methods Enzymol. 183, 252 278. Smit, A. F. A. (1996). Origin of interspersed repeats in the human genome. Curr. Opin. Genet. Devl. 6, 743 749. Smith, R. F., Wiese, B. A., Wojzynski, M. K., Davison, D. B., and Worley, K. C. (1996). BCM search launcher An integrated interface to molecular biology data base search and analysis services available on the World Wide Web. Genome Res. 6, 454 462. Snyder, E. E., and Stormo, G. D. (1995). Identification of coding regions in genomic DNA. J. Mol. Biol. 248, 1 18. Snyder, E. E., and Stormo, G. D. (1996). Identifying genes in genomic DNA sequences. In DNA and Protein Sequence Analysis: A Practical Approach. M. J. Bishop and C. J. Rawlings, Eds. (Oxford: 1RL Press), pp. 209 224. Solovyev, V., and Salamov, A. (1997). The Gene Finder computer tools for analysis of human and model organism genome sequences. In Proceedings of the Fifth International Conference on Intelligent Systems for Molecualr Biology. T. Gaasterland, P. Karp, K. Karplus, C. Ousounis, C. Sander, and A. Valencia, Eds. (Menlo Park, CA: AAA1 Press), pp. 294 302. Stormo, G. D. (1990). Finding protein coding regions in genomic sequences. Methods Enzymol. 183, 211 220. Tronche, F., Ringeisen, F., Blumenfeld, M., Yaniv, M., and Pontoglio, M. (1997). Analysis of the distribution of binding sites for a tissue specific transcription factor in the vertebrate genome. J. Mol. Biol. 266, 231 245. von Hippel, P. H. (1994). Protein DNA recognition: New perspectives and underlying themes. Science 263, 769 770. Wale, E., and Keller, W. (1996). The biochemistry of polyadenylation. Trends Biochem. Sci. 21, 247 250. Xu, Y., Einstein, J. R., Mural, R. J., Shah, M., and Uberbacher, E. C. (1994). An improved system for exon recognition and gene modeling in human NI-?è 15/161 0′y*ü GLc?,XNX#?"? 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1 0′y*ü GLc?,XNX#?"? .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om DNA sequences. In Proceedings of the Second International Conference on Interlligent Systems for Molecular Biology. R. Altman, D. Brutlag, P. Karp, R. Lathrop, and D. Seqrls, Eds. (Menlo Park, CA: AAA1 Press), pp. 376 383. Zhang, M. Q. (1997). Idnetification of protein coding regions in the human genome based on quadratic discriminant analysis. Proc. Natl. Acad. Sci. U.S.A. 94, 565 568. V T? NI ?? NI E¨ 2,? ) E¨ 29 X NI-?è 16/161 0′y*ü GLc?,XNX#?"? 2005 1 18file://E:\wcb\*ó(=μC:?A￥??1 0′y*ü GLc?,XNX#?"? .htm Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om Click to buy NOW! PDF XCHANGE ww w.d ocu track.c om