Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes

被引：42

作者：

Cummings, L ^{[1
]}

Riley, L ^{[1
]}

Black, L ^{[1
]}

Souvorov, A ^{[1
]}

Resenchuk, S ^{[1
]}

Dondoshansky, I ^{[1
]}

Tatusova, T ^{[1
]}

机构：

[1] Natl Lib Med, Natl Ctr Biotechnol Informat, NIH, Bethesda, MD 20894 USA

来源：

FEMS MICROBIOLOGY LETTERS | 2002年 / 216卷 / 02期

关键词：

genome analysis; sequence analysis; unfinished genome; bacterium; archaeon; eukaryote;

D O I：

10.1111/j.1574-6968.2002.tb11426.x

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

BLAST (Basic Local Alignment Search Tool) searches against DNA and protein sequence databases have become an indispensable tool for biomedical research. The proliferation of the genome sequencing projects is steadily increasing the fraction of genome-derived sequences in the public databases and their importance as a public resource. We report here the availability of Genomic BLAST, a novel graphical tool for simplifying BLAST searches against complete and unfinished genome sequences. This tool allows the user to compare the query sequence against a virtual database of DNA and/or protein sequences from a selected group of organisms with finished or unfinished genomes. The organisms for such a database can be selected using either a graphic taxonomy-based tree or an alphabetical list of organism-specific sequences. The first option is designed to help explore the evolutionary relationships among organisms within a certain taxonomy group when performing BLAST searches. The use of an alphabetical list allows the user to perform a more elaborate set of selections, assembling any given number of organism-specific databases from unfinished or complete genomes. This tool, available at the NCBI web site http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi, currently provides access to over 170 bacterial and archaeal genomes and over 40 eukaryotic genomes. (C) 2002 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.

引用

页码：133 / 138

页数：6

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