Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

Brian J. Haas; Arthur L. Delcher; Stephen M. Mount; Jennifer R. Wortman; Roger K. Smith; Linda I. Hannick; Rama Maiti; Catherine M. Ronning; Douglas B. Rusch; Christopher D. Town; Steven L. Salzberg; Owen White

doi:10.1093/nar/gkg770

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

Brian J. Haas, Arthur L. Delcher, Stephen M. Mount, Jennifer R. Wortman, Roger K. Smith, Linda I. Hannick, Rama Maiti, Catherine M. Ronning, Douglas B. Rusch, Christopher D. Town, Steven L. Salzberg, Owen White

School of Medicine

Research output: Contribution to journal › Article

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 ∼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.

Original language	English (US)
Pages (from-to)	5654-5666
Number of pages	13
Journal	Nucleic acids research
Volume	31
Issue number	19
DOIs	https://doi.org/10.1093/nar/gkg770
State	Published - Oct 1 2003

ASJC Scopus subject areas

Genetics

Access to Document

10.1093/nar/gkg770

Fingerprint Dive into the research topics of 'Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies'. Together they form a unique fingerprint.

Cite this

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. / Haas, Brian J.; 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.

In: Nucleic acids research, Vol. 31, No. 19, 01.10.2003, p. 5654-5666.

Research output: Contribution to journal › Article

Haas, Brian J. ; 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. / Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. In: Nucleic acids research. 2003 ; Vol. 31, No. 19. pp. 5654-5666.

@article{1ba8b0c7f6c749f3839b40082ede681d,

title = "Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies",

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 ∼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.",

author = "Haas, {Brian J.} and Delcher, {Arthur L.} and Mount, {Stephen M.} and Wortman, {Jennifer R.} and Smith, {Roger K.} and Hannick, {Linda I.} and Rama Maiti and Ronning, {Catherine M.} and Rusch, {Douglas B.} and Town, {Christopher D.} and Salzberg, {Steven L.} and Owen White",

year = "2003",

month = oct,

day = "1",

doi = "10.1093/nar/gkg770",

language = "English (US)",

volume = "31",

pages = "5654--5666",

journal = "Nucleic Acids Research",

issn = "1362-4962",

publisher = "Oxford University Press",

number = "19",

}

TY - JOUR

T1 - Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

AU - Haas, Brian J.

AU - Delcher, Arthur L.

AU - Mount, Stephen M.

AU - Wortman, Jennifer R.

AU - Smith, Roger K.

AU - Hannick, Linda I.

AU - Maiti, Rama

AU - Ronning, Catherine M.

AU - Rusch, Douglas B.

AU - Town, Christopher D.

AU - Salzberg, Steven L.

AU - White, Owen

PY - 2003/10/1

Y1 - 2003/10/1

N2 - 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 ∼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.

AB - 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 ∼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.

UR - http://www.scopus.com/inward/record.url?scp=0141905891&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0141905891&partnerID=8YFLogxK

U2 - 10.1093/nar/gkg770

DO - 10.1093/nar/gkg770

M3 - Article

C2 - 14500829

AN - SCOPUS:0141905891

VL - 31

SP - 5654

EP - 5666

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 1362-4962

IS - 19

ER -