Indexing Genomic Databases

Gina Cooper; Michael L. Raymer; Travis E. Doom; Dan E. Krane; Natsuhiko Futamura

doi:10.1109/BIBE.2004.1317395

Indexing Genomic Databases

Gina Cooper, Michael L. Raymer, Travis E. Doom, Dan E. Krane, Natsuhiko Futamura

Research output: Contribution to conference › Poster

Abstract

Current biological sequence comparison tools utilize full database searches to find approximate matches between a database and a query. A new approach to sequence comparisons can be performed by indexing the database using a novel indexing scheme. An indexed scheme can immediately eliminate highly mismatched sequences thereby improving performance and accuracy. iBlast is proposed as an indexed version of BLAST. In its initial implementation, iBlast uses a sequence-based index to catalog genomic databases in an NCR Teradata RDBMS. Several types of indexes and querying methods are explored to determine the most efficient solution utilizing the parallel nature of the Teradata system. Significant speedups were obtained and are explained in further detail in this paper. Future indexing methods based on prokaryotic and eukaryotic genome structures are also proposed.

Original language	American English
DOIs	https://doi.org/10.1109/BIBE.2004.1317395
State	Published - May 1 2004
Event	Proceedings of the Fourth IEEE Symposium on Bioinformatics and Bioengineering - Duration: May 1 2004 → …

Conference

Conference	Proceedings of the Fourth IEEE Symposium on Bioinformatics and Bioengineering
Period	5/1/04 → …

Disciplines

Bioinformatics
Communication
Communication Technology and New Media
Computer Sciences
Databases and Information Systems
Life Sciences
OS and Networks
Physical Sciences and Mathematics
Science and Technology Studies
Social and Behavioral Sciences

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10.1109/BIBE.2004.1317395License: CC BY

Indexing Genomic DatabasesFinal published version, 161 KBLicense: CC BY

Cite this

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title = "Indexing Genomic Databases",

abstract = " Current biological sequence comparison tools utilize full database searches to find approximate matches between a database and a query. A new approach to sequence comparisons can be performed by indexing the database using a novel indexing scheme. An indexed scheme can immediately eliminate highly mismatched sequences thereby improving performance and accuracy. iBlast is proposed as an indexed version of BLAST. In its initial implementation, iBlast uses a sequence-based index to catalog genomic databases in an NCR Teradata RDBMS. Several types of indexes and querying methods are explored to determine the most efficient solution utilizing the parallel nature of the Teradata system. Significant speedups were obtained and are explained in further detail in this paper. Future indexing methods based on prokaryotic and eukaryotic genome structures are also proposed.",

author = "Gina Cooper and Raymer, {Michael L.} and Doom, {Travis E.} and Krane, {Dan E.} and Natsuhiko Futamura",

year = "2004",

month = may,

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doi = "10.1109/BIBE.2004.1317395",

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note = "Proceedings of the Fourth IEEE Symposium on Bioinformatics and Bioengineering ; Conference date: 01-05-2004",

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AU - Cooper, Gina

AU - Raymer, Michael L.

AU - Doom, Travis E.

AU - Krane, Dan E.

AU - Futamura, Natsuhiko

PY - 2004/5/1

Y1 - 2004/5/1

N2 - Current biological sequence comparison tools utilize full database searches to find approximate matches between a database and a query. A new approach to sequence comparisons can be performed by indexing the database using a novel indexing scheme. An indexed scheme can immediately eliminate highly mismatched sequences thereby improving performance and accuracy. iBlast is proposed as an indexed version of BLAST. In its initial implementation, iBlast uses a sequence-based index to catalog genomic databases in an NCR Teradata RDBMS. Several types of indexes and querying methods are explored to determine the most efficient solution utilizing the parallel nature of the Teradata system. Significant speedups were obtained and are explained in further detail in this paper. Future indexing methods based on prokaryotic and eukaryotic genome structures are also proposed.

AB - Current biological sequence comparison tools utilize full database searches to find approximate matches between a database and a query. A new approach to sequence comparisons can be performed by indexing the database using a novel indexing scheme. An indexed scheme can immediately eliminate highly mismatched sequences thereby improving performance and accuracy. iBlast is proposed as an indexed version of BLAST. In its initial implementation, iBlast uses a sequence-based index to catalog genomic databases in an NCR Teradata RDBMS. Several types of indexes and querying methods are explored to determine the most efficient solution utilizing the parallel nature of the Teradata system. Significant speedups were obtained and are explained in further detail in this paper. Future indexing methods based on prokaryotic and eukaryotic genome structures are also proposed.

UR - https://corescholar.libraries.wright.edu/knoesis/921

U2 - 10.1109/BIBE.2004.1317395

DO - 10.1109/BIBE.2004.1317395

M3 - Poster

T2 - Proceedings of the Fourth IEEE Symposium on Bioinformatics and Bioengineering

Y2 - 1 May 2004

ER -

Indexing Genomic Databases

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