FGENES 1 FGENESH 4 FGENESH++ 14 FGENESH+18 FGENESB 20 FGENESV 22 FGENES-M 24 BESTORF 25 PROTCOMP26 BPROM 30 SPLICEDB 33 SCAN2 35 PDISORDER36 SPL37 NSITE 38 TSSP39 PLANTPROM 40 PROMH42 Other FGENESH43 Various programs74 FGENES Bioinformatics 2005 21(9)1776-1781 doi101093bioinformaticsbti283 Gene finding for the helical cytokines Darrell Conklin Betty Haldeman and Zeren Gao 1 2 2

1Department of Computing City University London United Kingdom 2ZymoGenetics Inc Seattle USA To whom correspondence should be addressed For comparison purposes three other gene finding methods were also run on the same dataset Fgenes v16 (Solovyev et al 1994) Genscan v10 (Burge and Karlin Genes Chromosomes and Cancer Volume 43 Issue 1 Pages 83 ndash 94 Published Online 18 Feb 2005 Molecular cloning and characterization of FBXO47 a novel gene containing an F-box domain located in the 17q12 band deleted in papillary renal cell carcinoma

Barbara Simon-Kayser 1 Catherine Scoul 1 Karine Renaudin 2 Pascal Jezequel 3 Olivier Bouchot 4 Jeacuterocircme Rigaud 4 Steacutephane Bezieau 1

1Laboratoire dEtude du Polymorphisme de l ADN Faculteacute de Meacutedecine Nantes France 2Service d anatomo-pathologie Hocirctel-Dieu Centre Hospitalier Universitaire Nantes France 3Centre de Recherche de Lutte Contre le Cancer Reneacute Gauducheau Saint Herblain France 4Service durologie Hocirctel-Dieu Centre Hospitalier Universitaire Nantes France

Sequence data from this article have been deposited with the GenBank Data Library under Accession No AY700575 html) GrailExp (httpgrailIsdornlgovgrailexp) Fgenes (httpgenomicsanger acukgfgfshtml) and Genmark (httpwww2ebiacukgenemark)

Journal of Neurobiology Volume 63 Issue 3 Pages 235 ndash 254 Published Online 4 Mar 2005 Shaw potassium channel genes in Drosophila James J L Hodge 1 2 James C Choi 2 Cahir J OKane 1 Leslie C Griffith 2

1Department of Genetics University of Cambridge Downing Site Cambridge CB2 3EH United Kingdom 2Department of Biology and Volen Center for Complex Systems Brandeis University MS008 415 South Street Waltham Massachusetts 02454-9110 Intronexon structure of Shawl was initially predicted using the FGENES program (Salamov and Solovyev 2000) on the Baylor College of Medicine Genefinder Current Proteomics January 2004 vol 1 no 1 pp 41-48(8) Annotation of the Human Genome by High-Throughput Sequence Analysis of Naturally Occurring Proteins Authors McGowan SJ1 Terrett J1 Brown CG1 Adam PJ1 Aldridge L1 Allen JC1 Amess B1 Andrews KA1 Barnes M1 Barnwell DE1 Affiliations 1 Oxford GlycoSciences plc The Forum 86 Milton Park Abingdon OX14 4RY UK The polymorphic lsquohypothetical transcriptomersquo was cons- tructed from transcripts predicted by FGENES FGENESH (Softberry Inc Mount Kisco NY USA) GENSCAN Nature Biotechnology 22 1146 ndash 1149 5-end SAGE for the analysis of transcriptional start sites Hashimoto et al (2004) from expressed sequence tag (EST) maps analysis of full-length cDNAs and computational annotation by Genscan Genie FGENES and other programs Hemoglobin Volume 28 Number 3 2004 255 ndash 259 An a-Thalassemia Phenotype in a Dutch Hindustani Caused by a New Point Mutation that Creates an Alternative Splice Donor Site in the First Exon of the a2-Globin Gene Cornelis L Harteveld A1 Pierre W Wijermans A2 Peter van Delft A1 Ellen Rasp A2 Hans L Haak A2 Piero C Giordano A1 A1 Hemoglobinopathies Laboratory Leiden University Medical Center PO Box 9503 2300 Leiden The Netherlands A2 Leyenburg Hospital The Hague The Netherlands and GRAIL gap2 (Gene Recognition and Assembly Internet Link Sequence exploration and gene discovery Version 13) Genefinder GENSCAN Fgenes and HMMGene Journal of Medical Genetics 200441e52 Genomic organisation of the UDP-N-acetylglucosamine-1-phosphotransferase gamma subunit (GNPTAG) and its mutations in mucolipidosis III

A Raas-Rothschild R Bargal O Goldman E Ben-Asher J E M Groener A Toutain E Stemmer Z Ben-Neriah H Flusser F A Beemer M Penttinen T Olender A J J T Rein G Bach and M Zeigler

1 1 1 2 3 4

1 1 5 6 7 2 8

1 11 Department of Human Genetics Hadassah University Medical Center Jerusalem Israel 2 Department of Molecular Genetics Weizmann Institute of Science Rehovot Israel 3 Departments of Pediatrics and Clinical Genetics Leiden University Medical Center Leiden The Netherlands 4 Service de Geacuteneacutetique CHU de Tours Hocircpital Bretonneau Tours France 5 Child Development Unit Soroka University Hospital Beer Sheva Israel 6 Department of Medical Genetics University Medical Center Utrecht The Netherlands 7 Clinical Genetics Unit Turku University Central Hospital Turku Finland 8 Division of Pediatric Cardiology Hadassah University Medical Center Jerusalem Israel Correspondence to A Raas-Rothschild MD Department of Human Genetics Hadassah University Hospital Jerusalem 91120 Israel annickmdhujiacil third intron is 9 kb This structure was consistent with the exon prediction of fgenes and Genscan Each splice donor and acceptor

FGENESH European Journal of Plant Pathology Issue Volume 112 Number 1 Date May 2005 Pages 23 - 29 DOI 101007s10658-004-7088-7 Leptosphaeria maculans a fungal pathogen of Brassica napus secretes a subtilisin-like serine protease Leanne M Wilson1 and Barbara J Howlett1

1 School of Botany The University of Melbourne Parkville Victoria 3010 Australia DNA and cDNA sequences were compared to identify intron positions which confirmed those predicted by FGENESH gene prediction software (wwwsoftberrycom) Current Genetics Issue Volume 47 Number 5 Date May 2005 Pages 307 ndash 315 DOI 101007s00294-004-0559-8 During attachment Phytophthora spores secrete proteins containing thrombospondin type 1 repeats Andrea V Robold1 and Adrienne R Hardham1

(1) Plant Cell Biology Group Research School of Biological Sciences The Australian National University Canberra ACT 2601 Australia infohtml) The DNA sequence was searched for introns using the soft- ware program FGENESH (httpwwwsoftberry comberryphtml Microbiology 151 (2005) 1499-1505 DOI 101099mic027759-0 Overproduction purification and characterization of FgaPT2 a dimethylallyltryptophan synthase from Aspergillus fumigatus Inge A Unsoumlld and Shu-Ming Li Pharmazeutische Biologie Pharmazeutisches Institut Eberhard-Karls-Universitaumlt Tuumlbingen Auf der Morgenstelle 8 72076 Tuumlbingen Germany Correspondence Shu-Ming Li shumingliuni-tuebingende FGENESH (Softberry wwwsoftberrycomberryphtml) and the DNASIS software package (version 21 Hitachi Software Engineering) were used for intron prediction Eukaryotic Cell March 2005 p 526-535 Vol 4 No 3 doi101128EC43526-5352005 Sex-Specific Homeodomain Proteins Sxi1 and Sxi2a Coordinately Regulate Sexual Development in Cryptococcus neoformans Christina M Hull1 Marie-Josee Boily and Joseph Heitman 1 12

Department of Molecular Genetics and Microbiology1 the Howard Hughes Medical Institute Duke University Medical Center Durham North Carolina2 Received 14 January 2005 Accepted 14 January 2005 Corresponding author Mailing address 322 CARL Building Box 3546 Department of Molecular Genetics and Microbiology 100 Research Dr Duke University Medical Center Durham NC 27710 Phone (919) 684-2824 Fax (919) 684-5458 E-mail heitm001dukeedu Present address Departments of Biomolecular Chemistry and Medical Microbiology amp

Immunology University of WisconsinmdashMadison Madison WI 53706

Sequence manipulations Splice predictions of candidate gene sequences for SXI2a were facilitated with a Softberry algorithm (wwwsoftberrycom)

Plant Mol Biol 2005 Feb57(3)445-60 Evaluation of five ab initio gene prediction programs for the discovery of maize genes Yao H Guo L Fu Y Borsuk LA Wen TJ Skibbe DS Cui X Scheffler BE Cao J Emrich SJ Ashlock DA Schnable PS Department of Genetics Development and Cell Biology Iowa State University Ames 50011-3650 USA hellipThe five programs were used in conjunction with RT-PCR to identify and establish the structures of two new genes in the a1-sh2 interval of the maize genome FGENESH GeneMarkhmm and GENSCAN were tested on a larger data set consisting of maize assembled genomic islands (MAGIs) that had been aligned to ESTs FGENESH GeneMarkhmm and GENSCAN correctly predicted gene models in 773 625 and 371 MAGIs respectively out of the 1353 MAGIs that comprise data set 2hellip New Phytologist 167 (1) July 2005 239-247 doi101111j1469-8137200501392x Identification of perennial ryegrass (Lolium perenne (L)) and meadow fescue (Festuca pratensis (Huds)) candidate orthologous sequences to the rice Hd1(Se1) and barley HvCO1 CONSTANS-like genes through comparative mapping and microsynteny P Armstead L Skoslasht L B Turner K Skoslasht I S Donnison M O Humphreys and I P King Author for correspondence Ian Armstead Tel +44 (0)1970 823108 Fax +44 (0)1970 823242 Email ianarmsteadbbsrcacuk Predictions of mRNA and protein sequences were carried out using fgenesh and fgenesh+ software ( http wwwsoftberrycom berryphtml ) Plant Physiology May 2005 Vol 138 pp 38-46 BIOINFORMATICS-PLANT DATABASES Databases and Information Integration for the Medicago truncatula Genome and Transcriptome1 Steven B Cannon John A Crow Michael L Heuer Xiaohong Wang Ethalinda KS Cannon Christopher Dwan Anne-Francoise Lamblin Jayprakash Vasdewani Joann Mudge Andrew Cook John Gish Foo Cheung Steve Kenton Timothy M Kunau Douglas Brown Gregory D May Dongjin Kim Douglas R Cook Bruce A Roe Chris D Town Nevin D Young and Ernest F Retzel

2 3

Department of Plant Pathology University of Minnesota St Paul Minnesota 55108 (SBC XW EKSC JV JM NDY) Center for Computational Genomics and Bioinformatics University of Minnesota Minneapolis Minnesota 55455 (JAC MLH CD AFL TMK

EFR) Department of Plant Pathology University of California Davis California 95616 (AC JG DJK DRC) The Institute for Genomic Research Rockville Maryland 20850 (FC CDT) Department of Chemistry and Biochemistry University of Oklahoma Norman Oklahoma 73019 (BAR SK) Plant Biology Division The Samuel Roberts Noble Foundation Ardmore Oklahoma 73401 (GDM) and North Carolina State University Fungal Genomics Laboratory Department of Plant Pathology Raleigh North Carolina 27695 (DB) 1 This work was supported by the National Science Foundation (awards DBIndash0321460 DBIndash0196197 DBIndash0110206 DBIndash9975806 and DBIndash9872565) by the US Department of Agriculture Cooperative State Research Education and Extension ServiceNational Research Initiative Program and by the Samuel Noble Roberts Foundation 2 Present address BioTeam Inc Cambridge MA 3 Present address University of Minnesota Cancer Center MMC 806 420 Delaware St SE Minneapolis MN 55455 wwwplantphysiolorgcgidoi101104pp104059204 Corresponding author e-mail ernestccgbumnedu fax 612ndash626ndash6069 Received December 31 2004 returned for revision March 4 2005 accepted March 21 2005 Annotation involves a multi-institution pipeline relying on Medicago-trained FGENESH (Salamov and Solovyev 2000 ) predictions the EuGene (Foissac et al Plant Physiology May 2005 Vol 138 pp 18-26 BIOINFORMATICS-PLANT DATABASES The Institute for Genomic Research Osa1 Rice Genome Annotation Database1 Qiaoping Yuan Shu Ouyang Aihui Wang Wei Zhu Rama Maiti Haining Lin John Hamilton Brian Haas Razvan Sultana Foo Cheung Jennifer Wortman and C Robin Buell

2

The Institute for Genomic Research Rockville Maryland 20850 1 This work (on rice genome annotation) was supported by the National Science Foundation (grant no DBIndash0321538 to CRB) and the US Department of Agriculture (grant no 2003ndash35317ndash13173 to CRB) 2 Present address Laboratory of Neurogenetics NIAAA NIH 5625 Fishers Lane Suite 3532 MSC 9412 Bethesda MD 20892 wwwplantphysiolorgcgidoi101104pp104059063 Corresponding author e-mail rbuelltigrorg fax 301ndash838ndash0208 Received December 31 2004 returned for revision February 24 2005 accepted March 21 2005 The ab initio gene finders used in the rice EGC pipeline include FGENESH (monocot matrix Salamov and Solovyev 2000 ) GeneMarkhmm (rice matrix Lukashin and Genome Research 15577-582 2005 Closing in on the C elegans ORFeome by cloning TWINSCAN predictions Chaochun Wei Philippe Lamesch Manimozhiyan Arumugam Jennifer Rosenberg Ping Hu Marc Vidal and Michael R Brent

1 2 1 2

1 2 13

1 Laboratory for Computational Genomics and Department of Computer Science and Engineering Washington University St Louis Missouri 63130 USA 2 Center for Cancer Systems Biology Dana-Farber Cancer Institute and Department of Genetics Harvard Medical School Boston Massachusetts 02115 USA

3 Corresponding author E-mail brentcsewustledu fax (314) 935-7302 Finally we compared TWINSCAN with two other gene-prediction systems that have recently been developed for nematodesndashFGENESH (Salamov and Solovyev 2000 Plant Physiology April 2005 Vol 137 pp 1174-1181 UPDATE ON SEQUENCING MEDICAGO TRUNCATULA AND LOTUS JAPONICUS Sequencing the Genespaces of Medicago truncatula and Lotus japonicus1 Nevin D Young Steven B Cannon Shusei Sato Dongjin Kim Douglas R Cook Chris D Town Bruce A Roe and Satoshi Tabata Department of Plant Pathology University of Minnesota St Paul Minnesota 55108 (NDY SBC) Kazusa DNA Research Institute Kisarazu Chiba 292ndash0818 Japan (SS ST) Department of Plant Pathology University of California Davis California 95616 (DRC DK) The Institute for Genomic Research Rockville Maryland 20850 (CDT) and Department of Chemistry and Biochemistry University of Oklahoma Norman Oklahoma 73019 (BAR) 1 The US component of the Medicago truncatula sequencing effort was initially supported by a grant from the Samuel Roberts Noble Foundation to BAR Current support comes from National Science Foundation Plant Genome Research Program (grant no 0110206 to DRC DK CDT and NDY and grant no 0321460 to NDY BAR and CDT) Funding for Lotus japonicus sequencing comes from the Kazusa DNA Research Institute Foundation wwwplantphysiolorgcgidoi101104pp104057034 Corresponding author e-mail nevinyumnedu fax 612ndash625ndash9728 hellip (These estimates are based on Fgenesh predictions [Salamov and Solovyev 2000 ] using a Mt-trained matrix retaining peptides with a BLASTP match at 10endash4 to the UniProt NREF100 database of peptides [Apweiler et al 2004 ] This estimate for Lj differs from the published value of 1 gene per 101 kb [Asamizu et al 2003a ] due to the use here of the Fgenesh gene-calling algorithm so Mt and Lj could be compared directly)hellip hellipThis estimate increases to 6500 when Lj genes are predicted by the Mt-trained Fgenesh algorithm described earlierhellip International Journal of CancerVolume 109 Issue 1 Pages 71 - 75Cancer Genetics Candidate regions of tumor suppressor locus on chromosome 9q311 in gastric cancer Naoto Kakinuma 1 Kazuyoshi Kohu 1 2 Masaaki Sato 1 Tatsuya Yamada 3 Motowo Nakajima 1 Tetsu Akiyama 2 Susumu Ohwada 3 Yasuhiko Shibanaka 1

1Novartis Pharma Tsukuba Research Institute Ibaraki Japan 2Laboratory of Molecular and Genetic Information Institute for Molecular and Cellular Biosciences University of Tokyo Tokyo Japan 3Second Department of Surgery Gunma University School of Medicine Gunma Japan email Yasuhiko Shibanaka (yasuhikoshibanakapharmanovartiscom) Correspondence to Yasuhiko Shibanaka Novartis Pharma Tsukuba Research Institute Ohkubo 8 Tsukuba-shi Ibaraki 300-2611 Japan Fax +81-29-865-2281

predict the genes between D9S277 and D9S127 in 9q311 the gene prediction tools also in the UCSC Genome Browser having Acembly Ensembl Fgenesh GenScan and Genome Research 1554-66 2005 Gene and alternative splicing annotation with AIR Liliana Florea145 Valentina Di Francesco2 Jason Miller1 Russell Turner1 Alison Yao2 Michael Harris2 Brian Walenz1 Clark Mobarry1 Gennady V Merkulov3 Rosane Charlab3 Ian Dew1 Zuoming Deng3 Sorin Istrail1 Peter Li2 and Granger Sutton1 1 Informatics Research Applied Biosystems Rockville Maryland 20850 USA 2 Advanced Solutions Celera Genomics Rockville Maryland 20850 USA 3 Scientific Content and Applications Celera Genomics Rockville Maryland 20850 USA Ab initio prediction programs such as GenScan (Burge and Karlin 1997 ) FGenesH (Salamov and Solovyev 2000 ) Genie (Kulp et al Nucleic Acids Research 2005 Vol 33 Database issue D399-D402 SilkDB a knowledgebase for silkworm biology and genomics Jing Wang Qingyou Xia Ximiao He Mingtao Dai Jue Ruan Jie Chen Guo Yu Haifeng Yuan Yafeng Hu Ruiqiang Li Tao Feng Chen Ye Cheng Lu Jun Wang Songgang Li Gane Ka-Shu Wong Huanming Yang Jian Wang Zhonghuai Xiang Zeyang Zhou and Jun Yu

1 2 34 3 34 3 3

3 3 3 3 3 2 135

1 36 35 35 2

2 35

1 College of Life Sciences Peking University Beijing 100871 China 2 The Key Sericultural Laboratory of Agricultural Ministry Southwest Agricultural University Chongqing 400716 China 3 Beijing Genomics Institute (BGI) Chinese Academy of Sciences (CAS) Beijing Airport Industrial Zone-B6 Beijing 101300 China 4 Graduate School of the Chinese Academy of Sciences Yuquan Road 19A Beijing 100039 China 5 Key Laboratory of Bioinformatics of Zhejiang Province Hangzhou Genomics Institute James D Watson Institute of Genome Sciences of Zhejiang University Hangzhou 310007 China and 6 Department of Medicine University of Washington Genome Center Seattle WA 98195 USA To whom correspondence should be addressed Tel +86 10 80481455 Fax +86 10 80498676 Email junyugenomicsorgcn Correspondence may also be addressed to Zeyang Zhou Tel +86 23 68251123 Fax +86 23 68251128 Email zyzhouswaucqcn The authors wish it to be known that in their opinion the first three authors should be regarded as joint First Authors BGF is a self-developed ab initio program based on GenScan (9) and FgeneSH (10) and was successfully utilized for our rice genome annotation (11) Clinical Cancer Research Vol 11 4029-4036 June 1 2005 Imaging Diagnosis Prognosis A Molecular Signature in Superficial Bladder Carcinoma Predicts Clinical Outcome Lars Dyrskjoslasht Karsten Zieger Mogens Kruhoslashffer Thomas Thykjaer Jens L Jensen Hanne Primdahl Natasha Aziz Niels Marcussen Klaus Moslashller and Torben F Oslashrntoft

1 12 15 15 4

1 6 3 2 1

Authors Affiliations 1 Molecular Diagnostic Laboratory Department of Clinical Biochemistry 2 Department of Urology and 3 University Institute of Pathology Aarhus University Hospital 4 Departments of Theoretical Statistics

and Mathematical Sciences University of Aarhus 5 Aros Applied Biotechnology Aarhus Denmark and 6 Eos BiotechnologyProtein Design Labs Fremont California Requests for reprints Torben F Oslashrntoft Molecular Diagnostic Laboratory Department of Clinical Biochemistry Aarhus University Hospital Skejby DK-8200 Aarhus N Denmark Phone 45-89495100 Fax 45-89496018 E-mail orntoftkiaudk array comprising 59619 probe sets representing 46000 unique sequences including known genes expressed sequence tag clusters and FGENESH-predicted exons BMC Evolutionary Biology 2005 51 doi1011861471-2148-5-1 Research article The WRKY transcription factor superfamily its origin in eukaryotes and expansion in plants Yuanji Zhang and Liangjiang Wang Address Plant Biology Division The Samuel Roberts Noble Foundation Ardmore OK 73402 USA Email Yuanji Zhang - yjzhangnobleorg Liangjiang Wang - Kevinlwangaolcom Corresponding author Despite minor differences in the gene structure prediction both gene prediction programs FGENESH and GENSCAN agree on the major features of the protein Nature Immunology 2005 v6 n3 The immunoglobulin heavy-chain locus in zebrafish identification and expression of a previously hellip N Danilova J Bussmann K Jekosch LA Steiner - - naturecom Nature Immunology Full text access provided to Googlebot Access by Web Services PLoS Biol 2005 June 3(6) e181 Published online 2005 May 24 doi 101371journalpbio0030181 RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons Vladimir V Kapitonov 1 and Jerzy Jurka 1

1Genetic Information Research Institute Mountain View California United States of America David Nemazee Academic EditorScripps Research Institute United States of America

Corresponding author Vladimir V Kapitonov vladimirgirinstorg Jerzy Jurka jurkagirinstorg Using FGENESH [33] we detected that the RAG1 corendashlike open reading frame (ORF) in the contig 29068 forms a terminal exon (positions 1154ndash2947) of an Genetics Published Articles Ahead of Print published on February 16 2005 as 101534genetics104036327 Identification and Characterization of Regions of the Rice Genome Associated with Broad- Spectrum Quantitative Disease Resistance Randall J Wisser Qi Sundagger Scot H Hulbertsect Stephen Kresovich and Rebecca J Nelsondaggerdagger 1 Department of Plant Breeding and Genetics Institute for Genomic Diversity Cornell University Ithaca New York 14853 daggerComputational Biology Service Unit Cornell Theory

Center Cornell University Ithaca New York 14853 sectDepartment of Plant Pathology Kansas State University Manhattan Kansas 66506 and daggerdaggerDepartment of Plant Pathology Cornell University Ithaca New York 14853 1Corresponding author Rebecca J Nelson Department of Plant Pathology Cornell University 321 Plant Science Ithaca NY 14853 Email rjn7cornelledu GENSCAN (B URGE and K ARLIN 1997) and FGENESH (S ALAMOV and S OLOVYEV 2001) to predict open reading frames Further searches against Plant Physiology January 2005 Vol 137 pp 176-189 Annotations and Functional Analyses of the Rice WRKY Gene Superfamily Reveal Positive and Negative Regulators of Abscisic Acid Signaling in Aleurone Cells1[w]

Zhen Xie Zhong-Lin Zhang Xiaolu Zou Jie Huang Paul Ruas Daniel Thompson and Qingxi J Shen

2 23

Department of Biological Sciences University of Nevada Las Vegas Nevada 891541 This work was supported by the US Department of Agriculture (grant no 02ndash35301ndash12066) by the National Institutes of Health (Biomedical Research Infrastructure Network seed grant no P20 RR16464) and by the University of Las Vegas Nevada (start-up funds to QJS) XZ was supported by a National Science Foundation Experimental Program to Stimulate Competitive

Research (EPSCoR) Integrative Approaches to Abiotic Stress (EPSndash0132556) graduate assistantship and Z-LZ by a National Science Foundation EPSCoR Advanced Computing in Environmental Sciences postdoctoral fellowship 2 These authors contributed equally to the paper 3 Present address Department of Plant and Microbial Biology University of California Berkeley CA 94720 and Plant Gene Expression Center US Department of Agriculture Albany CA 94710 [w] The online version of this article contains Web-only data First of all three genes (OsWRKY41 -43 and -44) were reannotated using FGENESH (wwwsoftberrycom) because the first introns of these genes were too small PLoS Biol 3(6) e181 (2005) RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons Vladimir V Kapitonov1 Jerzy Jurka1 1 Genetic Information Research Institute Mountain View California United States of America To whom correspondence should be addressed E-mail vladimirgirinstorg (VVK) E-mail jurkagirinstorg (JJ) Using FGENESH [33] we detected that the RAG1 corendashlike open reading frame (ORF) in the contig 29068 forms a terminal exon (positions 1154ndash2947) of an Plant and Cell Physiology 2005 46(1)3-13 doi101093pcppci503 From Mapping to Sequencing Post-sequencing and Beyond Takuji Sasaki Takashi Matsumoto Baltazar A Antonio and Yoshiaki Nagamura 1

National Institute of Agrobiological Sciences 2-1-2 Kannondai Tsukuba Ibaraki 305-8602 Japan 1 Corresponding author E-mail tsasakiniasaffrcgojp

The gene predictions by programs such as Genescan (Burge and Karlin 1997 ) FGENESH [see Appendix 1 (4)] and Genemark [see Appendix 1 (5)] BLAST (Altschul et Improving the nutritional value of Golden Rice through increased pro-vitamin A content JA Paine CA Shipton S Chaggar RM Howells MJ hellip - Nature Biotechnology 2005 - naturecom Arabidopsis thaliana psy and rice psy (AY024351) genes identified genomic sequences of similarity in which genes were predicted using FGENESH algorithm with Genetics Published Articles Ahead of Print published on January 16 2005 as 101534genetics104035543 THE GENETIC BASIS FOR INFLORESCENCE VARIATION BETWEEN FOXTAIL AND GREEN MILLET (POACEAE) Andrew N Doust Katrien M Devosdagger1 Mike D Gadberry Mike D Galedagger amp Elizabeth A Kellogg University of Missouri-St Louis Department of Biology One University Boulevard St Louis MO 63121 USA daggerJohn Innes Centre Norwich Research Park Colney Norwich NR4 7UH UK Current address University of Georgia-Athens Departments of Crop and Soil Sciences and Plant Biology Miller Plant Sciences Building Athens GA 30602 USA 1 Each of these contigs was scanned using FgeneSH (S ALAMOV and S OLOVYEV 2000) and open reading frames (ORFs) were translated and PLoS Biol 3(1) e13 January 2005

Sorghum Genome Sequencing by Methylation Filtration Joseph A Bedell1 Muhammad A Budiman2 Andrew Nunberg1 Robert W Citek1 Dan Robbins1 Joshua Jones2 Elizabeth Flick2 Theresa Rohlfing3 Jason Fries3 Kourtney Bradford3 Jennifer McMenamy3 Michael Smith4 Heather Holeman4 Bruce A Roe5 Graham Wiley5 Ian F Korf6 Pablo D Rabinowicz7 Nathan Lakey8 W Richard McCombie9 Jeffrey A Jeddeloh4 Robert A Martienssen9 1 Bioinformatics Orion Genomics Saint Louis Missouri United States of America 2 Library Construction Orion Genomics Saint Louis Missouri United States of America 3 Sequencing Orion Genomics Saint Louis Missouri United States of America 4 Biomarkers Orion Genomics Saint Louis Missouri United States of America 5 Department of Chemistry and Biochemistry University of Oklahoma Norman Oklahoma United States of America 6 Genome Center University of California Davis California United States of America 7 The Institute for Genomic Research Rockville Maryland United States of America 8 Business Orion Genomics Saint Louis Missouri United States of America 9 Cold Spring Harbor Laboratory Cold Spring Harbor New York United States of America additional parameters wordmask=seg lcmask M=1 N=ndash1 Q=3 R=3 kap E=1e-10 hspmax=0 To look for potentially novel genes we used Fgenesh (httpwww BMC Genomics 2005 611 doi1011861471-2164-6-11 FAM20 an evolutionarily conserved family of secreted proteins expressed in hematopoietic cells Demet Nalbant1 Hyewon Youn1 3 S Isil Nalbant1 Savitha Sharma1 Everardo Cobos2 3 Elmus G Beale1 Yang Du1 and Simon C Williams1 3 1Department of Cell Biology and Biochemistry Texas Tech University Health Sciences Center

Lubbock Texas 79430 USA 2Department of Internal Medicine Texas Tech University Health Sciences Center Lubbock Texas 79430 USA 3Southwest Cancer Center at University Medical Center Lubbock Texas 79430 USA These results were compared against genes assembled by two gene prediction programs FGENESH httpwwwsoftberrycomberryphtml and GENSCAN httpgenesmit Plant Physiology July 2005 Vol 138 pp 1205-1215 Complex Organization and Evolution of the Tomato Pericentromeric Region at the FER Gene Locus1[w] Romain Guyot Xudong Cheng Yan Su Zhukuan Cheng Edith Schlagenhauf Beat Keller and Hong-Qing Ling

2 2

Institute of Plant Biology University of Zurich 8008 Zurich Switzerland (RG ES BK H-QL) and Institute of Genetics and Developmental Biology Chinese Academy of Sciences Chaoyang District Beijing 100101 China (XC YS ZC H-QL) Putative genes were determined by a combination of coding region prediction software (GENSCAN FGENESH and MZEF with Arabidopsis andor monocot matrix J Gen Virol 86 (2005) 973-983 DOI 101099vir080833-0 Cloning characterization and analysis by RNA interference of various genes of the Chelonus inanitus polydnavirus Marianne Bonvin Dorothee Marti Stefan Wyder Dejan Kojic Marc Annaheim and Beatrice Lanzrein Institute of Cell Biology University of Berne Baltzerstrasse 4 CH-3012 Bern Switzerland Correspondence Beatrice Lanzrein beatricelanzreinizbunibech 12g1forw (5-GAGTCCATGCCGAATGTCAC-3) and 12g1rev (5-CTTCTTGCACAGCGACGAAC-3) were set to amplify the middle region of 12g1 as predicted with FGENESH 10 and The Plant Cell 17343-360 (2005) Evolution of DNA Sequence Nonhomologies among Maize Inbreds Stephan Brunner Kevin Fengler Michele Morgante Scott Tingey and Antoni Rafalski a1 a b a a

a DuPont Crop Genetics Research Wilmington Delaware 19880-353 b Universitaacute degli Studi di Udine Dipartimento di Scienze Agrarie ed Ambientali 33100 Udine Italy 1 To whom correspondence should be addressed E-mail stephanbrunnercgrdupontcom fax 302-695-2726 PNAS | February 1 2005 | vol 102 | no 5 | 1566-1571 Published online before print January 24 2005 101073pnas0409421102 A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome

Mark Yandell Adina M Bailey Sima Misra ShengQiang Shu Colin Wiel Martha Evans-Holm Susan E Celniker and Gerald M Rubin para para Howard Hughes Medical Institute and Department of Molecular and Cell Biology University of California Life Sciences Addition Berkeley CA 94720-3200 and paraDepartment of Genome Sciences Lawrence Berkeley National Laboratory One Cyclotron Road Mailstop 64-121 Berkeley CA 94720 genes based on a microarray-based approach that involved hybridizing randomly primed cDNA against probes corresponding to a large set of FGENESH predictions Insect Molecular Biology Volume 14 Issue 2 Page 113 - 119 April 2005 doi101111j1365-2583200400536x Detection and analysis of alternative splicing in the silkworm by aligning expressed sequence tags with the genomic sequence X-F Zha Q-Y Xia P Zhao J Li J Duan Z-L Wang J-F Qian and Z-H Xiang Correspondence Dr Qing-You Xia The Key Sericultural Laboratory of Agricultural Ministry Southwest Agricultural University Chongqing 400716 China Tel +86 23 68250748 fax +86 23 68251128 e-mail xiaqyswaucqcn previously predicted silkworm genes in the genomic sequences by BGF a newly developed program based on GENSCAN (Burge amp Karlin 1997) and Fgenesh (Salamov amp Microbiology 151 (2005) 2199-2207 DOI 101099mic027962-0 Overproduction purification and characterization of FtmPT1 a brevianamide F prenyltransferase from Aspergillus fumigatus Alexander Grundmann and Shu-Ming Li Pharmazeutische Biologie Pharmazeutisches Institut Eberhard-Karls-Universitaumlt Tuumlbingen Auf der Morgenstelle 8 72076 Tuumlbingen Germany Correspondence Shu-Ming Li shumingliuni-tuebingende FGENESH (Softberry Inc httpwwwsoftberrycomberryphtml) and the DNASIS software package (version 21 Hitachi Software Engineering) were used for