Annotation of the Arabidopsis Genome

Plant Physiology

Volumn 132, Issue 2, 2003, Pages 461-468

  Wortman, Jennifer R ^a   Haas, Brian J ^a   Hannick, Linda I ^a   Smith Jr , Roger K ^a   Maiti, Rama ^a   Ronning, Catherine M ^a   Chan, Agnes P ^a   Yu, Chunhui ^a   Ayele, Mulu ^a   Whitelaw, Catherine A ^a   White, Owen R ^a   Town, Christopher D ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; EMBRYOPHYTA;

EID: 0038797803     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.103.022251     Document Type: Review

References (25)

1. AGI (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
2. Bairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28: 45-48
3. Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T (2001) Multiple snoRNA gene clusters from Arabidopsis. RNA 7: 1817-1832
4. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94
5. Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL et al. (2002) Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419: 512-519
6. Hebsgaard SM, Korning PG, Tolstrup N, Engelbrecht J, Rouze P, Brunak S (1996) Splice site prediction in Arabidopsis thaliana pre mRNA by combining local and global sequence information. Nucleic Acids Res 24: 3439-3452
7. Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell RB, White O, Salzberg SL (2002) Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol 3: reaearch 0029.1-research 0029.12
8. Huang X, Adams MD, Zhou H, Kerlavage AR (1997) A tool for analyzing and annotating genomic sequences. Genomics 46: 37-45
9. Kan Z, Rouchka EC, Gish WR, States DJ (2001) Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Res 11: 889-900
10. Llave C, Kasschau KD, Rector MA, Carrington JC (2002) Endogenous and silencing-associated small RNAs in plants. Plant Cell 14: 1605-1619
11. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964
12. Lukashin AV, Borodovsky M (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26: 1107-1115
13. MacIntosh GC, Wilkerson C, Green PJ (2001) Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs. Plant Physiol 127: 765-776
14. Mozo T, Dewar K, Dunn P, Ecker JR, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier-Ewert S et al. (1999) A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat Genet 22: 271-275
15. Mural RJ, Adams MD, Myers EW, Smith HO, Gabor Miklos GL, Wides R, Halpern A, Li PW, Sutton GG, Nadeau J et al. (2002) A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 296: 1661-1671
16. Pertea M, Lin X, Salzberg SL (2001) GeneSplicer: a new computational method for splice site prediction. Nucleic Acids Res 29: 1185-1190
17. Quackenbush J, Liang F, Holt I, Pertea G, Upton J (2000) The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res 28: 141-145
18. Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M et al. (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31: 224-228
19. Round EK, Flowers SK, Richards EJ (1997) Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure. Genome Res 7: 1045-1053
20. Salzberg SL, Pertea M, Delcher AL, Gardner MJ, Tettelin H (1999) Interpolated Markov models for eukaryotic gene finding. Genomics 59: 24-31
21. Schoof H, Zaccaria P, Gundlach H, Lemcke K, Rudd S, Kolesov G, Arnold R, Mewes HW, Mayer KF (2002) MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res 30: 91-93
22. Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W (2003) Human-mouse alignments with BLASTZ. Genome Res 13: 103-107
23. Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R (1998) Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res 26: 320-322
24. The Gene Ontology Consortium (2000) Gene Ontology: tool for unification of biology. Nat Genet 25: 25-29
25. Xiao Y-L, Malik M, Whitelaw CA, Town CD (2002) Cloning and sequencing of cDNAs for hypothetical proteins from chromosome 2 of Arabidopsis thaliana. Plant Physiol 130: 2118-2128