RSDB - A database of repetitive elements in complete genomes

Jorng Tzong Horng; Jia Hwang Lin; Cheng Yan Kao

RSDB - A database of repetitive elements in complete genomes

Jorng Tzong Horng, Jia Hwang Lin, Cheng Yan Kao

Department of Computer Science and Information Engineering

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

5 Scopus citations

Abstract

Repeat Sequence Database (RSDB) stores repeat sequences in genomes. RSDB differs from other databases with repeat sequences found by conventional experimental results because the repeat sequences recorded in RSDB are explored via a mathematical algorithm. This work designs and implements a database to store complete and comprehensive repeat sequences. This is despite the fact that the database contains direct, inverted and palindromic repetitive sequences, and each repetitive sequence has a variable length ranging from seven to several hundred nucleotides. A customized format of a flat file is defined for the database so that it can be easily translated into some other genome database systems. In addition, use of the database is facilitated by providing some searching tools based on the features, positions, patterns, accession numbers and sequence identifiers of repeat sequences. These searching tools are constructed mainly on SQL query statements to access the database through the Internet. As widely anticipated, the quantity of repetitive sequences of the database will become increasingly larger.

Original language	English
Title of host publication	Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technology, CBGIST 2001
Editors	C.H. Wu, P.P. Wang, J.T.L. Wang
Pages	220-224
Number of pages	5
State	Published - 2001
Event	Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technology, GBGIST 2001 - Durham, NC, United States Duration: 15 Mar 2001 → 17 Mar 2001

Publication series

Name	Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technolgoy, CBGIST 2001

Conference

Conference	Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technology, GBGIST 2001
Country/Territory	United States
City	Durham, NC
Period	15/03/01 → 17/03/01

Cite this

Horng, J. T., Lin, J. H., & Kao, C. Y. (2001). RSDB - A database of repetitive elements in complete genomes. In C. H. Wu, P. P. Wang, & J. T. L. Wang (Eds.), Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technology, CBGIST 2001 (pp. 220-224). (Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technolgoy, CBGIST 2001).

Horng, Jorng Tzong ; Lin, Jia Hwang ; Kao, Cheng Yan. / RSDB - A database of repetitive elements in complete genomes. Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technology, CBGIST 2001. editor / C.H. Wu ; P.P. Wang ; J.T.L. Wang. 2001. pp. 220-224 (Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technolgoy, CBGIST 2001).

@inproceedings{23e13949a223479c91ceb65d2aeef6f5,

title = "RSDB - A database of repetitive elements in complete genomes",

abstract = "Repeat Sequence Database (RSDB) stores repeat sequences in genomes. RSDB differs from other databases with repeat sequences found by conventional experimental results because the repeat sequences recorded in RSDB are explored via a mathematical algorithm. This work designs and implements a database to store complete and comprehensive repeat sequences. This is despite the fact that the database contains direct, inverted and palindromic repetitive sequences, and each repetitive sequence has a variable length ranging from seven to several hundred nucleotides. A customized format of a flat file is defined for the database so that it can be easily translated into some other genome database systems. In addition, use of the database is facilitated by providing some searching tools based on the features, positions, patterns, accession numbers and sequence identifiers of repeat sequences. These searching tools are constructed mainly on SQL query statements to access the database through the Internet. As widely anticipated, the quantity of repetitive sequences of the database will become increasingly larger.",

author = "Horng, {Jorng Tzong} and Lin, {Jia Hwang} and Kao, {Cheng Yan}",

year = "2001",

language = "???core.languages.en_GB???",

isbn = "0970789009",

series = "Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technolgoy, CBGIST 2001",

pages = "220--224",

editor = "C.H. Wu and P.P. Wang and J.T.L. Wang",

booktitle = "Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technology, CBGIST 2001",

note = "null ; Conference date: 15-03-2001 Through 17-03-2001",

}

Horng, JT, Lin, JH & Kao, CY 2001, RSDB - A database of repetitive elements in complete genomes. in CH Wu, PP Wang & JTL Wang (eds), Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technology, CBGIST 2001. Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technolgoy, CBGIST 2001, pp. 220-224, Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technology, GBGIST 2001, Durham, NC, United States, 15/03/01.

RSDB - A database of repetitive elements in complete genomes. / Horng, Jorng Tzong; Lin, Jia Hwang; Kao, Cheng Yan.

Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technology, CBGIST 2001. ed. / C.H. Wu; P.P. Wang; J.T.L. Wang. 2001. p. 220-224 (Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technolgoy, CBGIST 2001).

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

TY - GEN

T1 - RSDB - A database of repetitive elements in complete genomes

AU - Horng, Jorng Tzong

AU - Lin, Jia Hwang

AU - Kao, Cheng Yan

PY - 2001

Y1 - 2001

N2 - Repeat Sequence Database (RSDB) stores repeat sequences in genomes. RSDB differs from other databases with repeat sequences found by conventional experimental results because the repeat sequences recorded in RSDB are explored via a mathematical algorithm. This work designs and implements a database to store complete and comprehensive repeat sequences. This is despite the fact that the database contains direct, inverted and palindromic repetitive sequences, and each repetitive sequence has a variable length ranging from seven to several hundred nucleotides. A customized format of a flat file is defined for the database so that it can be easily translated into some other genome database systems. In addition, use of the database is facilitated by providing some searching tools based on the features, positions, patterns, accession numbers and sequence identifiers of repeat sequences. These searching tools are constructed mainly on SQL query statements to access the database through the Internet. As widely anticipated, the quantity of repetitive sequences of the database will become increasingly larger.

AB - Repeat Sequence Database (RSDB) stores repeat sequences in genomes. RSDB differs from other databases with repeat sequences found by conventional experimental results because the repeat sequences recorded in RSDB are explored via a mathematical algorithm. This work designs and implements a database to store complete and comprehensive repeat sequences. This is despite the fact that the database contains direct, inverted and palindromic repetitive sequences, and each repetitive sequence has a variable length ranging from seven to several hundred nucleotides. A customized format of a flat file is defined for the database so that it can be easily translated into some other genome database systems. In addition, use of the database is facilitated by providing some searching tools based on the features, positions, patterns, accession numbers and sequence identifiers of repeat sequences. These searching tools are constructed mainly on SQL query statements to access the database through the Internet. As widely anticipated, the quantity of repetitive sequences of the database will become increasingly larger.

UR - http://www.scopus.com/inward/record.url?scp=1842560561&partnerID=8YFLogxK

M3 - 會議論文篇章

AN - SCOPUS:1842560561

SN - 0970789009

T3 - Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technolgoy, CBGIST 2001

SP - 220

EP - 224

BT - Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technology, CBGIST 2001

A2 - Wu, C.H.

A2 - Wang, P.P.

A2 - Wang, J.T.L.

Y2 - 15 March 2001 through 17 March 2001

ER -

Horng JT, Lin JH, Kao CY. RSDB - A database of repetitive elements in complete genomes. In Wu CH, Wang PP, Wang JTL, editors, Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technology, CBGIST 2001. 2001. p. 220-224. (Proceedings of the Atlantic Symposium on Computational Biology and Genome Information Systems and Technolgoy, CBGIST 2001).

RSDB - A database of repetitive elements in complete genomes

Abstract

Publication series

Conference

Fingerprint

Cite this