Annotation of porcine expressed sequence tags and creation of porcine-humane orthologous gene resources

Yuandan Zhang; C K Tuggle; M F Rothschild; K Garwood; W Beavis

Annotation of porcine expressed sequence tags and creation of porcine-humane orthologous gene resources

Yuandan Zhang, C K Tuggle, M F Rothschild, K Garwood, W Beavis

Animal Genetics and Breeding Unit

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

A collection of 113,497 public Expressed Sequence Tags (ESTs) from Genbank dbEST were utilized. Nucleotide similarities between pig ESTs and human genes were determined by cDNA alignment against 97,100 human UniGene sequences. Available data for pig-on-human comparative maps and homology between pig and human chromosomes were then used to predict pig EST assignments on pig chromosomes. The similarities among pig ESTs and 3,331 pig genes retrieved from GenBank were also examined. Results showed that 28,113 pig ESTs hits 10,258 human UniGenes, and 6,254 pig ESTs hits 1,362 pig gene sequences (score >= 200). As a results of this comparative analysis, a porcine expressed sequence tagged (EST) database, a set of tools for EST analyses and a web query tool for public access to this database were developed. This database is comprised of a number of tables covering the EST profile, alignment similarity, human ortholog information on cytogenetic, and RH locations. Interactive web query interfaces are developed for public access to the EST database.

Original language	English
Title of host publication	Proceedings of the Association for the Advancement of Animal Breeding and Genetics
Editors	Abigail Henderson
Place of Publication	Armidale, Australia
Publisher	Association for the Advancement of Animal Breeding and Genetics (AAABG)
Pages	98-102
Volume	15
ISBN (Print)	0958629927
Publication status	Published - 2003
Event	AAABG 2003: 15th Conference of the Association for the Advancement of Animal Breeding and Genetics - Melbourne, Australia Duration: 7 Jul 2003 → 11 Jul 2003

Conference

Conference	AAABG 2003: 15th Conference of the Association for the Advancement of Animal Breeding and Genetics
City	Melbourne, Australia
Period	7/07/03 → 11/07/03

Keywords

Animal Breeding

Access to Document

https://hdl.handle.net/1959.11/4351

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Zhang, Y., Tuggle, C. K., Rothschild, M. F., Garwood, K., & Beavis, W. (2003). Annotation of porcine expressed sequence tags and creation of porcine-humane orthologous gene resources. In A. Henderson (Ed.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics (Vol. 15, pp. 98-102). Association for the Advancement of Animal Breeding and Genetics (AAABG). https://hdl.handle.net/1959.11/4351

Zhang, Yuandan ; Tuggle, C K ; Rothschild, M F et al. / Annotation of porcine expressed sequence tags and creation of porcine-humane orthologous gene resources. Proceedings of the Association for the Advancement of Animal Breeding and Genetics. editor / Abigail Henderson. Vol. 15 Armidale, Australia : Association for the Advancement of Animal Breeding and Genetics (AAABG), 2003. pp. 98-102

@inproceedings{7e4a6b493ed546789cca7b3008c690e5,

title = "Annotation of porcine expressed sequence tags and creation of porcine-humane orthologous gene resources",

abstract = "A collection of 113,497 public Expressed Sequence Tags (ESTs) from Genbank dbEST were utilized. Nucleotide similarities between pig ESTs and human genes were determined by cDNA alignment against 97,100 human UniGene sequences. Available data for pig-on-human comparative maps and homology between pig and human chromosomes were then used to predict pig EST assignments on pig chromosomes. The similarities among pig ESTs and 3,331 pig genes retrieved from GenBank were also examined. Results showed that 28,113 pig ESTs hits 10,258 human UniGenes, and 6,254 pig ESTs hits 1,362 pig gene sequences (score >= 200). As a results of this comparative analysis, a porcine expressed sequence tagged (EST) database, a set of tools for EST analyses and a web query tool for public access to this database were developed. This database is comprised of a number of tables covering the EST profile, alignment similarity, human ortholog information on cytogenetic, and RH locations. Interactive web query interfaces are developed for public access to the EST database.",

keywords = "Animal Breeding",

author = "Yuandan Zhang and Tuggle, \{C K\} and Rothschild, \{M F\} and K Garwood and W Beavis",

year = "2003",

language = "English",

isbn = "0958629927",

volume = "15",

pages = "98--102",

editor = "Abigail Henderson",

booktitle = "Proceedings of the Association for the Advancement of Animal Breeding and Genetics",

publisher = "Association for the Advancement of Animal Breeding and Genetics (AAABG)",

note = "AAABG 2003: 15th Conference of the Association for the Advancement of Animal Breeding and Genetics ; Conference date: 07-07-2003 Through 11-07-2003",

}

Zhang, Y, Tuggle, CK, Rothschild, MF, Garwood, K & Beavis, W 2003, Annotation of porcine expressed sequence tags and creation of porcine-humane orthologous gene resources. in A Henderson (ed.), Proceedings of the Association for the Advancement of Animal Breeding and Genetics. vol. 15, Association for the Advancement of Animal Breeding and Genetics (AAABG), Armidale, Australia, pp. 98-102, AAABG 2003: 15th Conference of the Association for the Advancement of Animal Breeding and Genetics, Melbourne, Australia, 7/07/03. <https://hdl.handle.net/1959.11/4351>

Annotation of porcine expressed sequence tags and creation of porcine-humane orthologous gene resources. / Zhang, Yuandan; Tuggle, C K; Rothschild, M F et al.
Proceedings of the Association for the Advancement of Animal Breeding and Genetics. ed. / Abigail Henderson. Vol. 15 Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG), 2003. p. 98-102.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Annotation of porcine expressed sequence tags and creation of porcine-humane orthologous gene resources

AU - Zhang, Yuandan

AU - Tuggle, C K

AU - Rothschild, M F

AU - Garwood, K

AU - Beavis, W

PY - 2003

Y1 - 2003

N2 - A collection of 113,497 public Expressed Sequence Tags (ESTs) from Genbank dbEST were utilized. Nucleotide similarities between pig ESTs and human genes were determined by cDNA alignment against 97,100 human UniGene sequences. Available data for pig-on-human comparative maps and homology between pig and human chromosomes were then used to predict pig EST assignments on pig chromosomes. The similarities among pig ESTs and 3,331 pig genes retrieved from GenBank were also examined. Results showed that 28,113 pig ESTs hits 10,258 human UniGenes, and 6,254 pig ESTs hits 1,362 pig gene sequences (score >= 200). As a results of this comparative analysis, a porcine expressed sequence tagged (EST) database, a set of tools for EST analyses and a web query tool for public access to this database were developed. This database is comprised of a number of tables covering the EST profile, alignment similarity, human ortholog information on cytogenetic, and RH locations. Interactive web query interfaces are developed for public access to the EST database.

AB - A collection of 113,497 public Expressed Sequence Tags (ESTs) from Genbank dbEST were utilized. Nucleotide similarities between pig ESTs and human genes were determined by cDNA alignment against 97,100 human UniGene sequences. Available data for pig-on-human comparative maps and homology between pig and human chromosomes were then used to predict pig EST assignments on pig chromosomes. The similarities among pig ESTs and 3,331 pig genes retrieved from GenBank were also examined. Results showed that 28,113 pig ESTs hits 10,258 human UniGenes, and 6,254 pig ESTs hits 1,362 pig gene sequences (score >= 200). As a results of this comparative analysis, a porcine expressed sequence tagged (EST) database, a set of tools for EST analyses and a web query tool for public access to this database were developed. This database is comprised of a number of tables covering the EST profile, alignment similarity, human ortholog information on cytogenetic, and RH locations. Interactive web query interfaces are developed for public access to the EST database.

KW - Animal Breeding

UR - http://trove.nla.gov.au/work/22223828?selectedversion=NBD24379203

UR - http://www.aaabg.org/livestocklibrary/2003/98-102.pdf

M3 - Conference contribution

SN - 0958629927

VL - 15

SP - 98

EP - 102

BT - Proceedings of the Association for the Advancement of Animal Breeding and Genetics

A2 - Henderson, Abigail

PB - Association for the Advancement of Animal Breeding and Genetics (AAABG)

CY - Armidale, Australia

T2 - AAABG 2003: 15th Conference of the Association for the Advancement of Animal Breeding and Genetics

Y2 - 7 July 2003 through 11 July 2003

ER -

Zhang Y, Tuggle CK, Rothschild MF, Garwood K, Beavis W. Annotation of porcine expressed sequence tags and creation of porcine-humane orthologous gene resources. In Henderson A, editor, Proceedings of the Association for the Advancement of Animal Breeding and Genetics. Vol. 15. Armidale, Australia: Association for the Advancement of Animal Breeding and Genetics (AAABG). 2003. p. 98-102

Annotation of porcine expressed sequence tags and creation of porcine-humane orthologous gene resources

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