References

  1. The FlyBase Consortium: The FlyBase database of the Drosophila genome projects and community literature.

    Nucleic Acids Res 2002, 30:106-108. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  2. FlyBase: a database of the Drosophila Genome [http://www.flybase.org]
  3. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, et al.: The genome sequence of Drosophila melanogaster.

    Science 2000, 287:2185-2195. PubMed Abstract | Publisher Full Text OpenURL

  4. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, et al.: Comparative genomics of the eukaryotes.

    Science 2000, 287:2204-2215. PubMed Abstract | Publisher Full Text OpenURL

  5. Rubin GM, Hong L, Brokstein P, Evans-Holm M, Frise E, Stapleton M, Harvey DA: A Drosophila complementary DNA resource.

    Science 2000, 287:2222-2224. PubMed Abstract | Publisher Full Text OpenURL

  6. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL: GenBank.

    Nucleic Acids Res 2002, 30:17-20. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  7. GenBank via ftp [http://www.ncbi.nlm.nih.gov/Genbank/GenBankFtp.html]
  8. Stoesser G, Baker W, van den Broek A, Camon E, Garcia-Pastor M, Kanz C, Kulikova T, Leinonen R, Lin Q, Lombard V, et al.: The EMBL nucleotide sequence database.

    Nucleic Acids Res 2002, 30:21-26. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  9. EMBL nucleotide sequence database [http://www.ebi.ac.uk/embl]
  10. Tateno Y, Imanishi T, Miyazaki S, Fukami-Kobayashi K, Saitou N, Sugawara H, Gojobori T: DNA Data Bank of Japan (DDBJ) for genome scale research in life science.

    Nucleic Acids Res 2002, 30:27-30. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  11. DDBJ DNA Databank of Japan [http://www.ddbj.nig.ac.jp]
  12. Mungall CJ, Misra S, Berman BP, Carlson J, Frise E, Harris N, Marshall B, Shu S, Kaminker JS, Prochnik SE, et al.: An integrated computational pipeline and database to support whole-genome sequence annotation.

    Genome Biol 2002, 3:research0081.1-0081.11. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  13. Bairoch A, Apweiler R: The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

    Nucleic Acids Res 2000, 28:45-48. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  14. Karlin S, Bergman A, Gentles AJ: Genomics. Annotation of the Drosophila genome.

    Nature 2001, 411:259-260. PubMed Abstract | Publisher Full Text OpenURL

  15. Gopal S, Schroeder M, Pieper U, Sczyrba A, Aytekin-Kurban G, Bekiranov S, Fajardo JE, Eswar N, Sanchez R, Sali A, et al.: Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome.

    Nat Genet 2001, 27:337-340. PubMed Abstract | Publisher Full Text OpenURL

  16. Andrews J, Bouffard GG, Cheadle C, Lu J, Becker KG, Oliver B: Gene discovery using computational and microarray analysis of transcription in the Drosophila melanogaster testis.

    Genome Res 2000, 10:2030-2043. PubMed Abstract | Publisher Full Text OpenURL

  17. Celniker SE, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, Patel S, Adams M, Champe M, Dugan SP, Frise E, et al.: Finishing a whole-genome shotgun: Release 3 of the Drosophila euchromatic genome sequence.

    Genome Biol 2002, 3:research0079.1-0079.14. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  18. Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, et al.: The transposable elements of the Drosophila melanogaster euchromatin - a genomics perspective.

    Genome Biol 2002, 3:research0084.1-0084.20. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  19. Lewis SE, Searle SMJ, Harris N, Gibson M, Iyer V, Richter J, Wiel C, Bayraktaroglu L, Birney E, Crosby L, et al.: Apollo: a sequence annotation editor.

    Genome Biol 2002, 3:research0082.1-0082.14. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  20. Reese MG, Kulp D, Tammana H, Haussler D: Genie - gene finding in Drosophila melanogaster.

    Genome Res 2000, 10:529-538. PubMed Abstract | Publisher Full Text OpenURL

  21. Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA.

    J Mol Biol 1997, 268:78-94. PubMed Abstract | Publisher Full Text OpenURL

  22. Wu-BLAST [http://blast.wustl.edu]
  23. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool.

    J Mol Biol 1990, 215:403-410. PubMed Abstract | Publisher Full Text OpenURL

  24. Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W: A computer program for aligning a cDNA sequence with a genomic DNA sequence.

    Genome Res 1998, 8:967-974. PubMed Abstract | Publisher Full Text OpenURL

  25. Hoskins RA, Smith CD, Carlson JW, Carvalho AB, Halpern A, Kaminker JS, Kennedy C, Mungall CJ, Sullivan BA, Sutton GG, et al.: Heterochromatic sequences in a Drosophila whole-genome shotgun assembly.

    Genome Biol 2002, 3:research0085.1-0085.16. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  26. The C. elegans Sequencing Consortium: Genome sequence of the nematode C. elegans: a platform for investigating biology.

    Science 1998, 282:2012-2018. PubMed Abstract | Publisher Full Text OpenURL

  27. Lin X, Kaul S, Rounsley S, Shea TP, Benito MI, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, et al.: Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.

    Nature 1999, 402:761-768. PubMed Abstract | Publisher Full Text OpenURL

  28. Ensembl human genome browser [http://www.ensembl.org/Homo_sapiens]
  29. Stapleton M, Liao G, Brokstein P, Hong L, Carninci P, Shiraki T, Hayashizaki Y, Champe M, Pacleb J, Wan K, et al.: The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes.

    Genome Res 2002, 12:1294-1300. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  30. Stapleton M, Carlson J, Brokstein J, Yu C, Champe M, George R, Guarin H, Kronmiller B, Pacleb J, Park S, et al.: A Drosophila full-length cDNA resource.

    Genome Biol 2002, 3:research0080.1-0080.8. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  31. Wilkin MB, Becker MN, Mulvey D, Phan I, Chao A, Cooper K, Chung HJ, Campbell ID, MacIntyre M, Macintyre R: Drosophila dumpy is a gigantic extracellular protein required to maintain tension at epidermalcuticle attachment sites.

    Curr Biol 2000, 10:559-567. PubMed Abstract | Publisher Full Text OpenURL

  32. Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

    Nucleic Acids Res 1997, 25:955-964. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  33. Wooley JC, Cone RD, Tartof D, Chung SY: Small nuclear ribonucleoprotein complexes of Drosophila melanogaster.

    Proc Natl Acad Sci USA 1982, 79:6762-6766. PubMed Abstract OpenURL

  34. Tycowski KT, Steitz JA: Non-coding snoRNA host genes in Drosophila: expression strategies for modification guide snoRNAs.

    Eur J Cell Biol 2001, 80:119-125. PubMed Abstract OpenURL

  35. Lowe TM, Eddy SR: A computational screen for methylation guide snoRNAs in yeast.

    Science 1999, 283:1168-1171. PubMed Abstract | Publisher Full Text OpenURL

  36. Shendure J, Church GM: Computational discovery of sense-antisense transcription in the human and mouse genomes.

    Genome Biol 2002, 3:research0044.1-0044.14. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  37. Echols N, Harrison P, Balasubramanian S, Luscombe NM, Bertone P, Zhang Z, Gerstein M: Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.

    Nucleic Acids Res 2002, 30:2515-2523. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  38. Mounsey A, Bauer P, Hope IA: Evidence suggesting that a fifth of annotated Caenorhabditis elegans genes may be pseudogenes.

    Genome Res 2002, 12:770-775. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  39. Stein L, Sternberg P, Durbin R, Thierry-Mieg J, Spieth J: WormBase: network access to the genome and biology of Caenorhabditis elegans.

    Nucleic Acids Res 2001, 29:82-86. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  40. WormBase, The Genome and Biology of C. elegans, Release WS88 [http://www.wormbase.org]
  41. Gu Z, Cavalcanti A, Chen FC, Bouman P, Li WH: Extent of gene duplication in the genomes of Drosophila, nematode, and yeast.

    Mol Biol Evol 2002, 19:256-262. PubMed Abstract | Publisher Full Text OpenURL

  42. De Gregorio E, Spellman PT, Rubin GM, Lemaitre B: Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays.

    Proc Natl Acad Sci USA 2001, 98:12590-12595. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  43. Krauss V, Reuter G: Two genes become one: the genes encoding heterochromatin protein Su(var)3-9 and translation initiation factor subunit eIF-2gamma are joined to a dicistronic unit in holometabolic insects.

    Genetics 2000, 156:1157-1167. PubMed Abstract | Publisher Full Text OpenURL

  44. Ashburner M, Misra S, Roote J, Lewis SE, Blazej R, Davis T, Doyle C, Galle R, George R, Harris N, et al.: An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region.

    Genetics 1999, 153:179-219. PubMed Abstract | Publisher Full Text OpenURL

  45. Spencer CA, Gietz RD, Hodgetts RB: Overlapping transcription units in the dopa decarboxylase region of Drosophila .

    Nature 1986, 322:279-281. PubMed Abstract OpenURL

  46. Kumar M, Carmichael GG: Antisense RNA: function and fate of duplex RNA in cells of higher eukaryotes.

    Microbiol Mol Biol Rev 1998, 62:1415-1434. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  47. Vanhee-Brossollet C, Vaquero C: Do natural antisense transcripts make sense in eukaryotes?

    Gene 1998, 211:1-9. PubMed Abstract | Publisher Full Text OpenURL

  48. Labrador M, Mongelard F, Plata-Rengifo P, Baxter EM, Corces VG, Gerasimova TI: Protein encoding by both DNA strands.

    Nature 2001, 409:1000. PubMed Abstract | Publisher Full Text OpenURL

  49. Dorn R, Reuter G, Loewendorf A: Transgene analysis proves mRNA trans-splicing at the complex mod(mdg4) locus in Drosophila.

    Proc Natl Acad Sci USA 2001, 98:9724-9729. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  50. Giniger E, Tietje K, Jan LY, Jan YN: lola encodes a putative transcription factor required for axon growth and guidance in Drosophila.

    Development 1994, 120:1385-1398. PubMed Abstract | Publisher Full Text OpenURL

  51. Read D, Butte MJ, Dernburg AF, Frasch M, Kornberg TB: Functional studies of the BTB domain in the Drosophila GAGA and Mod(mdg4) proteins.

    Nucleic Acids Res 2000, 28:3864-3870. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  52. Bell AC, West AG, Felsenfeld G: Insulators and boundaries: versatile regulatory elements in the eukaryotic genome.

    Science 2001, 291:447-450. PubMed Abstract | Publisher Full Text OpenURL

  53. Harvey AJ, Bidwai AP, Miller LK: Doom, a product of the Drosophila mod(mdg4) gene, induces apoptosis and binds to baculovirus inhibitor-of-apoptosis proteins.

    Mol Cell Biol 1997, 17:2835-2843. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  54. Pauli D, Tonka CH, Ayme-Southgate A: An unusual split Drosophila heat shock gene expressed during embryogenesis, pupation and in testis.

    J Mol Biol 1988, 200:47-53. PubMed Abstract OpenURL

  55. Schulz RA, Miksch JL, Xie XL, Cornish JA, Galewsky S: Expression of the Drosophila gonadal gene: alternative promoters control the germ-line expression of monocistronic and bicistronic gene transcripts.

    Development 1990, 108:613-622. PubMed Abstract OpenURL

  56. Andrews J, Smith M, Merakovsky J, Coulson M, Hannan F, Kelly LE: The stoned locus of Drosophila melanogaster produces a dicistronic transcript and encodes two distinct polypeptides.

    Genetics 1996, 143:1699-1711. PubMed Abstract OpenURL

  57. Brogna S, Ashburner M: The Adh-related gene of Drosophila melanogaster is expressed as a functional dicistronic messenger RNA: multigenic transcription in higher organisms.

    EMBO J 1997, 16:2023-2031. PubMed Abstract | Publisher Full Text OpenURL

  58. Niimi T, Yokoyama H, Goto A, Beck K, Kitagawa Y: A Drosophila gene encoding multiple splice variants of Kazal-type serine protease inhibitor-like proteins with potential destinations of mitochondria, cytosol and the secretory pathway.

    Eur J Biochem 1999, 266:282-292. PubMed Abstract | Publisher Full Text OpenURL

  59. Gray TA, Nicholls RD: Diverse splicing mechanisms fuse the evolutionarily conserved bicistronic MOCS1A and MOCS1B open reading frames.

    RNA 2000, 6:928-936. PubMed Abstract | Publisher Full Text OpenURL

  60. Liu H, Jang JK, Graham J, Nycz K, McKim KS: Two genes required for meiotic recombination in Drosophila are expressed from a dicistronic message.

    Genetics 2000, 154:1735-1746. PubMed Abstract | Publisher Full Text OpenURL

  61. Walker DL, Wang D, Jin Y, Rath U, Wang Y, Johansen J, Johansen KM: Skeletor, a novel chromosomal protein that redistributes during mitosis provides evidence for the formation of a spindle matrix.

    J Cell Biol 2000, 151:1401-1412. PubMed Abstract | Publisher Full Text OpenURL

  62. Levine F, Yee JK, Friedmann T: Efficient gene expression in mammalian cells from a dicistronic transcriptional unit in an improved retroviral vector.

    Gene 1991, 108:167-174. PubMed Abstract | Publisher Full Text OpenURL

  63. Peabody DS, Berg P: Termination-reinitiation occurs in the translation of mammalian cell mRNAs.

    Mol Cell Biol 1986, 6:2695-2703. PubMed Abstract OpenURL

  64. Oh SK, Scott MP, Sarnow P: Homeotic gene Antennapedia mRNA contains 5'-noncoding sequences that confer translational initiation by internal ribosome binding.

    Genes Dev 1992, 6:1643-1653. PubMed Abstract OpenURL

  65. Bergman CM, Pfeiffer BD, Rincón-Limas DE, Hoskins RA, Gnirke A, Mungall CJ, Wang AM, Kronmiller B, Pacleb J, Park S, et al.: Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome.

    Genome Biol 2002, 3:research0086.1-0086.20. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  66. Reese MG, Hartzell G, Harris NL, Ohler U, Abril JF, Lewis SE: Genome annotation assessment in Drosophila melanogaster .

    Genome Res 2000, 10:483-501. PubMed Abstract | Publisher Full Text OpenURL

  67. Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell RB, White O, Salzberg SL: Full-length messenger RNA sequences greatly improve genome annotation.

    Genome Biol 2002, 3:research0029.1-0029.12. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  68. Gaasterland T, Oprea M: Whole-genome analysis: annotations and updates.

    Curr Opin Struct Biol 2001, 11:377-381. PubMed Abstract | Publisher Full Text OpenURL

  69. Expressed Sequence Tags Database (dbEST) [http://www.ncbi.nlm.nih.gov/dbEST]
  70. Kans JA, Ouellette BF: Submitting DNA sequences to the databases.

    Methods Biochem Anal 2001, 43:65-81. PubMed Abstract | Publisher Full Text OpenURL

  71. Sequin - a DNA sequence submission and update tool [http://www.ncbi.nlm.nih.gov/Sequin]
  72. Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, et al.: InterPro - an integrated documentation resource for protein families, domains and functional sites.

    Bioinformatics 2000, 16:1145-1150. PubMed Abstract | Publisher Full Text OpenURL

  73. Spradling AC, Stern D, Beaton A, Rhem EJ, Laverty T, Mozden N, Misra S, Rubin GM: The Berkeley Drosophila Genome Project gene disruption project: single P-element insertions mutating 25% of vital Drosophila genes.

    Genetics 1999, 153:135-177. PubMed Abstract | Publisher Full Text OpenURL

  74. Apollo gene annotation tool: developer page [http://www.fruitfly.org/annot/apollo]
  75. BDGP: download BDGP sequence and annotation databases [http://www.fruitfly.org/sequence/download.html]
  76. FlyBase update form [http://www.fruitfly.org/cgi-bin/annot/FBupdate]
  77. Ohler U, Liao G-C, Niemann H, Rubin GM: Computational analysis of core promoters in the Drosophila genome.

    Genome Biol 2002, 3:research0087.1-0087.12. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

  78. Gene Ontology Consortium [http://www.geneontology.org]
  79. Mi H, Vandergriff J, Campbell MJ, Marechania A, Majoros W, Lewis S, Thomas PD, Ashburner M: Assessment of genome-wide protein function classification for Drosophila melanogaster.

    Genome Res, in press. OpenURL

  80. SWISS-PROT [http://www.ebi.ac.uk/swissprot]
  81. TrEMBL [http://www.ebi.ac.uk/trembl/index.html]
  82. BDGP re-annotation guidelines [http://www.fruitfly.org/annot/reannot-guidelines.html]
  83. SP-TrEMBL (SWALL, SWISS-PROT/TrEMBL/TrEMBLNEW) database [http://www.ebi.ac.uk/trembl]
  84. UniGene Mus musculus [http://www.ncbi.nlm.nih.gov/UniGene/query.cgi?ORG=Mm]
  85. TrEMBL Protein Database Statistics [http://www2.ebi.ac.uk/swissprot/sptr_stats]
  86. Zdobnov EM, Von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, et al.: Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster.

    Science 2002, 298:149-159. PubMed Abstract | Publisher Full Text OpenURL

  87. GFF format: an exchange format for feature description [http://www.sanger.ac.uk/Software/formats/GFF]