From owner-announce@net.bio.net Sun Oct 11 23:00:00 1998 Path: biosci!biosci!not-for-mail From: "Victor Solovyev" Newsgroups: bionet.announce Subject: New Prediction of Variants of gene structure FGENES-M Date: 12 Oct 1998 11:29:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 178 Sender: daemon@net.bio.net Approved: biosci-help@net.bio.net Distribution: world Message-ID: <9810041526.ZM5389@octane> NNTP-Posting-Host: net.bio.net New Prediction of Variants of gene structure FGENES-M ====================================================== Fgenes-M variant for mammalian sequences is available at CGG WEB site: http://genomic.sanger.ac.uk/gf/gf.html There are 2 reasons to predict several sub-optimal variants of gene structure (instead of only one): 1) Gene prediction algorithms for long genomic sequences are just 70-80% accurate in average, therefore a real structure might have the score slightly lower than the produced optimal variant (and you will never see it for such case having just 1 prediction); 2) Mammalian genes often have alternative splicing and your sequenced mRNA might not correspond to the predicted variant (in this case actually several gene structures are real). There are thousands of alternative gene structures is possible to generate and currently does not exist established way to generate variants exactly corresponding to the real ones. Fgenes-M variant was proved to be useful in helping provide a set of possible gene structures for further experimental testing in commercial gene hunting, therefore I decided to put it to WWW. FGENES-M 1.5 - Pattern based Human Multiple variants of Gene structure prediction Algorithm outputs several suboptimal variants of predicted gene structure. In the current WWW server variant up to 10 structures of gene of multiple genes is provided. It is similar with FGENES and based on pattern recognition of different types of exons, promoters and polyA signals and by dynamic programming finding the optimal combination of them constructing a set of gene models along a given sequences You might compare a validity of a predicted variant using GENE WEIGHT, if it is close to the 1st optimal variant, than it worth to consider it. A simple example of Fgenes-M output: FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 1 Max var= 5 GENE WEIGHT: 24.1 G Str Feature Start End Weight ORF-start ORF-end 1 + TSS 355 7.43 TATA 327 wTATA 21.08 LDF 0.56 1 + 1 CDSf 521 - 641 1.23 521 - 640 1 + 2 CDSi 1066 - 1362 2.08 1068 - 1361 1 + 3 CDSi 1860 - 2028 1.69 1862 - 2026 1 + 4 CDSi 2637 - 2802 2.74 2638 - 2802 1 + 5 CDSi 3558 - 3797 4.35 3558 - 3797 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 521 - 4247 369 a Ch+ MAGTVTEAWDVAVFAARRRNDEDDTTRDSLFTYTNSNNTRGPFEGPNYHIAPRWVYNITS VWMIFVVIASIFTNGLVLVATAKFKKLRHPLNWILVNLAIADLGETVIASTISVINQISG YFILGHPMCVLEGYTVSTCGISALWSLAVISWERWVVVCKPFGNVKFDAKLAVAGIVFSW VWSAVWTAPPVFGWSRYWPHGLKTSCGPDVFSGSDDPGVLSYMIVLMITCCFIPLAVILL CYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCWGPYTVFACFAAANPGY AFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKVDDGSELSSTSRTEVSS VSNSSVSPA FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 2 Max var= 5 GENE WEIGHT: 15.1 G Str Feature Start End Weight ORF-start ORF-end 1 + 1 CDSf 218 - 321 1.01 218 - 319 1 + 2 CDSi 984 - 1023 1.94 985 - 1023 1 + 3 CDSi 1860 - 2028 1.49 1860 - 2027 1 + 4 CDSi 2675 - 2802 1.00 2677 - 2802 1 + 5 CDSi 3558 - 3797 4.35 3558 - 3797 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 218 - 4247 265 a Ch+ MRQGGGQITAQLRDKTFKGFEDLVLQVRGLIRLGGNLLVDVCVVIAILVSQLSGPWPLYL GNAGSLSASPLEMSSSMPNWPWLALSSPGCGLLYGQHHPSLAGVDVFSGSDDPGVLSYMI VLMITCCFIPLAVILLCYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCW GPYTVFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKV DDGSELSSTSRTEVSSVSNSSVSPA FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 3 Max var= 5 GENE WEIGHT: 15.1 G Str Feature Start End Weight ORF-start ORF-end 1 + 1 CDSf 218 - 321 1.01 218 - 319 1 + 2 CDSi 984 - 1023 1.94 985 - 1023 1 + 3 CDSi 1860 - 2028 1.49 1860 - 2027 1 + 4 CDSi 2675 - 2802 1.00 2677 - 2802 1 + 5 CDSi 3558 - 3797 4.35 3558 - 3797 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 218 - 4247 265 a Ch+ MRQGGGQITAQLRDKTFKGFEDLVLQVRGLIRLGGNLLVDVCVVIAILVSQLSGPWPLYL GNAGSLSASPLEMSSSMPNWPWLALSSPGCGLLYGQHHPSLAGVDVFSGSDDPGVLSYMI VLMITCCFIPLAVILLCYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCW GPYTVFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKV DDGSELSSTSRTEVSSVSNSSVSPA FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 4 Max var= 5 GENE WEIGHT: 15.1 G Str Feature Start End Weight ORF-start ORF-end 1 + 1 CDSf 218 - 321 1.01 218 - 319 1 + 2 CDSi 984 - 1023 1.94 985 - 1023 1 + 3 CDSi 1860 - 2028 1.49 1860 - 2027 1 + 4 CDSi 2675 - 2802 1.00 2677 - 2802 1 + 5 CDSi 3558 - 3797 4.35 3558 - 3797 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 218 - 4247 265 a Ch+ MRQGGGQITAQLRDKTFKGFEDLVLQVRGLIRLGGNLLVDVCVVIAILVSQLSGPWPLYL GNAGSLSASPLEMSSSMPNWPWLALSSPGCGLLYGQHHPSLAGVDVFSGSDDPGVLSYMI VLMITCCFIPLAVILLCYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCW GPYTVFACFAAANPGYAFHPLAAALPAYFAKSATIYNPIIYVFMNRQFRNCIMQLFGKKV DDGSELSSTSRTEVSSVSNSSVSPA FGENES-M 1.5.0 Prediction of several variants of multiple genes Time: 214127.7 Date: 19981003 Seq name: ACU08131 Length of sequence: 5392 GC content: 0.46 Zone: 2 Number of predicted genes: 1 In +chain: 1 In -chain: 0 Number of predicted exons: 6 In +chain: 6 In -chain: 0 Predicted genes and exons in var: 5 Max var= 5 GENE WEIGHT: 13.9 G Str Feature Start End Weight ORF-start ORF-end 1 + TSS 355 7.43 TATA 327 wTATA 21.08 LDF 0.56 1 + 1 CDSf 521 - 641 1.23 521 - 640 1 + 2 CDSi 1066 - 1362 2.08 1068 - 1361 1 + 3 CDSi 1860 - 2028 1.69 1862 - 2026 1 + 4 CDSi 2637 - 2802 2.74 2638 - 2802 1 + 5 CDSi 3558 - 3668 0.99 3558 - 3668 1 + 6 CDSl 4131 - 4247 2.09 4131 - 4244 1 + PolA 4650 3.17 Predicted proteins: >FGENES 1.5 ACU08131 1 Multiexon gene 521 - 4247 326 a Ch+ MAGTVTEAWDVAVFAARRRNDEDDTTRDSLFTYTNSNNTRGPFEGPNYHIAPRWVYNITS VWMIFVVIASIFTNGLVLVATAKFKKLRHPLNWILVNLAIADLGETVIASTISVINQISG YFILGHPMCVLEGYTVSTCGISALWSLAVISWERWVVVCKPFGNVKFDAKLAVAGIVFSW VWSAVWTAPPVFGWSRYWPHGLKTSCGPDVFSGSDDPGVLSYMIVLMITCCFIPLAVILL CYLQVWLAIRAVAAQQKESESTQKAEKEVSRMVVVMIIAYCFCWGPYTFRNCIMQLFGKK VDDGSELSSTSRTEVSSVSNSSVSPA -- Victor Solovyev The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK Email: solovyev@sanger.ac.uk http://genomic.sanger.ac.uk Phone: 44-1223-494799 FAX: 44-1223-494919 .