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PMID: 14500829 Published · ppublish English Evaluation Study Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.

Nucleic acids research ·Vol. 31 ·No. 19 ·2003-10-01 ·Pages 5654-66

Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, Salzberg SL, White O

Abstract

The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble clusters of overlapping transcript alignments (ESTs and full-length cDNAs) into maximal alignment assemblies, thereby comprehensively incorporating all available transcript data and capturing subtle splicing variations. Complete and partial gene structures identified by this method were used to improve The Institute for Genomic Research Arabidopsis genome annotation (TIGR release v.4.0). The alignment assemblies permitted the automated modeling of several novel genes and >1000 alternative splicing variations as well as updates (including UTR annotations) to nearly half of the approximately 27 000 annotated protein coding genes. The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations.

MeSH Terms
Algorithms Alternative Splicing Arabidopsis/genetics,metabolism DNA, Complementary/analysis Expressed Sequence Tags Genome, Plant Introns Plant Proteins/genetics RNA, Plant/analysis,chemistry Sequence Alignment/methods Software Transcription, Genetic Untranslated Regions
Chemicals
DNA, Complementary Plant Proteins RNA, Plant Untranslated Regions
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
Haas Brian J
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA. [email protected]
Delcher Arthur L
Mount Stephen M
Wortman Jennifer R
Smith Roger K
Hannick Linda I
Maiti Rama
Ronning Catherine M
Rusch Douglas B
Town Christopher D
Salzberg Steven L
White Owen
References (43)
43 references, click to expand
  1. Non-AUG initiation of AGAMOUS mRNA translation in Arabidopsis thaliana.
    Mol Cell Biol. 1999 Dec;19(12):8505-12 PMID: 10567575
  2. Cloning and sequencing of cDNAs for hypothetical genes from chromosome 2 of Arabidopsis.
    Plant Physiol. 2002 Dec;130(4):2118-28 PMID: 12481096
  3. Using GeneWise in the Drosophila annotation experiment.
    Genome Res. 2000 Apr;10(4):547-8 PMID: 10779496
  4. The Arabidopsis splicing factor SR1 is regulated by alternative splicing.
    Plant Mol Biol. 2000 Mar;42(4):571-81 PMID: 10809003
  5. EST comparison indicates 38% of human mRNAs contain possible alternative splice forms.
    FEBS Lett. 2000 May 26;474(1):83-6 PMID: 10828456
  6. Optimal spliced alignment of homologous cDNA to a genomic DNA template.
    Bioinformatics. 2000 Mar;16(3):203-11 PMID: 10869013
  7. A large scale analysis of cDNA in Arabidopsis thaliana: generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries.
    DNA Res. 2000 Jun 30;7(3):175-80 PMID: 10907847
  8. Genomic sequence, splicing, and gene annotation.
    Am J Hum Genet. 2000 Oct;67(4):788-92 PMID: 10986039
  9. A new set of Arabidopsis expressed sequence tags from developing seeds. The metabolic pathway from carbohydrates to seed oil.
    Plant Physiol. 2000 Dec;124(4):1582-94 PMID: 11115876
  10. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species.
    Nucleic Acids Res. 2001 Jan 1;29(1):159-64 PMID: 11125077
  11. STACK: Sequence Tag Alignment and Consensus Knowledgebase.
    Nucleic Acids Res. 2001 Jan 1;29(1):234-8 PMID: 11125101
  12. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
    Nature. 2000 Dec 14;408(6814):796-815 PMID: 11130711
  13. Computational inference of homologous gene structures in the human genome.
    Genome Res. 2001 May;11(5):803-16 PMID: 11337476
  14. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs.
    Genome Res. 2001 May;11(5):889-900 PMID: 11337482
  15. Regulation of flowering in Arabidopsis by an FLC homologue.
    Plant Physiol. 2001 May;126(1):122-32 PMID: 11351076
  16. Genome-wide detection of alternative splicing in expressed sequences of human genes.
    Nucleic Acids Res. 2001 Jul 1;29(13):2850-9 PMID: 11433032
  17. Multiple forms of formamidopyrimidine-DNA glycosylase produced by alternative splicing in Arabidopsis thaliana.
    J Photochem Photobiol B. 2001 Aug 30;61(3):87-93 PMID: 11535407
  18. Spidey: a tool for mRNA-to-genomic alignments.
    Genome Res. 2001 Nov;11(11):1952-7 PMID: 11691860
  19. Alternative splicing and genome complexity.
    Nat Genet. 2002 Jan;30(1):29-30 PMID: 11743582
  20. Database resources of the National Center for Biotechnology.
    Nucleic Acids Res. 2003 Jan 1;31(1):28-33 PMID: 12519941
  21. Computational discovery of internal micro-exons.
    Genome Res. 2003 Jun;13(6A):1216-21 PMID: 12799353
  22. Annotation of the Arabidopsis genome.
    Plant Physiol. 2003 Jun;132(2):461-8 PMID: 12805579
  23. Refined annotation of the Arabidopsis genome by complete expressed sequence tag mapping.
    Plant Physiol. 2003 Jun;132(2):469-84 PMID: 12805580
  24. Improved tools for biological sequence comparison.
    Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444-8 PMID: 3162770
  25. Sex-lethal, a Drosophila sex determination switch gene, exhibits sex-specific RNA splicing and sequence similarity to RNA binding proteins.
    Cell. 1988 Dec 23;55(6):1037-46 PMID: 3144435
  26. Positive autoregulation of sex-lethal by alternative splicing maintains the female determined state in Drosophila.
    Cell. 1991 Apr 19;65(2):229-39 PMID: 2015624
  27. Complementary DNA sequencing: expressed sequence tags and human genome project.
    Science. 1991 Jun 21;252(5013):1651-6 PMID: 2047873
  28. An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana.
    Plant J. 1993 Dec;4(6):1051-61 PMID: 8281187
  29. Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones.
    Plant Physiol. 1994 Dec;106(4):1241-55 PMID: 7846151
  30. Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs.
    Plant J. 1996 Jan;9(1):101-24 PMID: 8580968
  31. The Arabidopsis thaliana cDNA sequencing projects.
    FEBS Lett. 1997 Mar 24;405(2):129-32 PMID: 9089275
  32. A comparison of expressed sequence tags (ESTs) to human genomic sequences.
    Nucleic Acids Res. 1997 Apr 15;25(8):1626-32 PMID: 9092672
  33. A tool for analyzing and annotating genomic sequences.
    Genomics. 1997 Nov 15;46(1):37-45 PMID: 9403056
  34. Analysis of EST-driven gene annotation in human genomic sequence.
    Genome Res. 1998 Apr;8(4):362-76 PMID: 9548972
  35. A computer program for aligning a cDNA sequence with a genomic DNA sequence.
    Genome Res. 1998 Sep;8(9):967-74 PMID: 9750195
  36. Alternative splicing of pre-mRNA: developmental consequences and mechanisms of regulation.
    Annu Rev Genet. 1998;32:279-305 PMID: 9928482
  37. Large-scale sequencing of plant genomes.
    Curr Opin Plant Biol. 1998 Apr;1(2):136-41 PMID: 10066574
  38. Comparison of gene indexing databases.
    Trends Genet. 1999 Apr;15(4):159-62 PMID: 10203827
  39. BLAT--the BLAST-like alignment tool.
    Genome Res. 2002 Apr;12(4):656-64 PMID: 11932250
  40. Functional annotation of a full-length Arabidopsis cDNA collection.
    Science. 2002 Apr 5;296(5565):141-5 PMID: 11910074
  41. Full-length messenger RNA sequences greatly improve genome annotation.
    Genome Biol. 2002;3(6):RESEARCH0029 PMID: 12093376
  42. Detection of Arabidopsis thaliana AtRAD1 cDNA variants and assessment of function by expression in a yeast rad1 mutant.
    Gene. 2002 Aug 21;296(1-2):1-9 PMID: 12383497
  43. Ab initio gene finding in Drosophila genomic DNA.
    Genome Res. 2000 Apr;10(4):516-22 PMID: 10779491
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkg770
Email
[email protected]
Published
2003-10-01
Pages
5654-66
Language
English
Region
England
NLM ID
0411011
PMCID
PMC206470
Subset
IM
Grants
NLM NIH HHS · R01 LM006845 · United States
NLM NIH HHS · R01-LM06845-04 · United States
External Links
PubMed source DOI: 10.1093/nar/gkg770 PMC Full Text View journal details
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