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Title: Curated BLAST for Genomes

Abstract

ABSTRACT Curated BLAST for Genomes finds candidate genes for a process or an enzymatic activity within a genome of interest. In contrast to annotation tools, which usually predict a single activity for each protein, Curated BLAST asks if any of the proteins in the genome are similar to characterized proteins that are relevant. Given a query such as an enzyme’s name or an EC number, Curated BLAST searches the curated descriptions of over 100,000 characterized proteins, and it compares the relevant characterized proteins to the predicted proteins in the genome of interest. In case of errors in the gene models, Curated BLAST also searches the six-frame translation of the genome. Curated BLAST is available at http://papers.genomics.lbl.gov/curated . IMPORTANCE Given a microbe’s genome sequence, we often want to predict what capabilities the organism has, such as which nutrients it requires or which energy sources it can use. Or, we know the organism has a capability and we want to find the genes involved. Scientists often use automated gene annotations to find relevant genes, but automated annotations are often vague or incorrect. Curated BLAST finds candidate genes for a capability without relying on automated annotations. First, Curated BLAST finds proteins (usually frommore » other organisms) whose functions have been studied experimentally and whose curated descriptions match a query. Then, it searches the genome of interest for similar proteins and returns a list of candidates. Curated BLAST is fast and often finds relevant genes that are missed by automated annotation.« less

Authors:
ORCiD logo; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1504291
Alternate Identifier(s):
OSTI ID: 1508064
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Published Article
Journal Name:
mSystems
Additional Journal Information:
Journal Name: mSystems Journal Volume: 4 Journal Issue: 2; Journal ID: ISSN 2379-5077
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; annotation

Citation Formats

Price, Morgan N., Arkin, Adam P., and Greene, ed., Casey S. Curated BLAST for Genomes. United States: N. p., 2019. Web. doi:10.1128/mSystems.00072-19.
Price, Morgan N., Arkin, Adam P., & Greene, ed., Casey S. Curated BLAST for Genomes. United States. doi:10.1128/mSystems.00072-19.
Price, Morgan N., Arkin, Adam P., and Greene, ed., Casey S. Tue . "Curated BLAST for Genomes". United States. doi:10.1128/mSystems.00072-19.
@article{osti_1504291,
title = {Curated BLAST for Genomes},
author = {Price, Morgan N. and Arkin, Adam P. and Greene, ed., Casey S.},
abstractNote = {ABSTRACT Curated BLAST for Genomes finds candidate genes for a process or an enzymatic activity within a genome of interest. In contrast to annotation tools, which usually predict a single activity for each protein, Curated BLAST asks if any of the proteins in the genome are similar to characterized proteins that are relevant. Given a query such as an enzyme’s name or an EC number, Curated BLAST searches the curated descriptions of over 100,000 characterized proteins, and it compares the relevant characterized proteins to the predicted proteins in the genome of interest. In case of errors in the gene models, Curated BLAST also searches the six-frame translation of the genome. Curated BLAST is available at http://papers.genomics.lbl.gov/curated . IMPORTANCE Given a microbe’s genome sequence, we often want to predict what capabilities the organism has, such as which nutrients it requires or which energy sources it can use. Or, we know the organism has a capability and we want to find the genes involved. Scientists often use automated gene annotations to find relevant genes, but automated annotations are often vague or incorrect. Curated BLAST finds candidate genes for a capability without relying on automated annotations. First, Curated BLAST finds proteins (usually from other organisms) whose functions have been studied experimentally and whose curated descriptions match a query. Then, it searches the genome of interest for similar proteins and returns a list of candidates. Curated BLAST is fast and often finds relevant genes that are missed by automated annotation.},
doi = {10.1128/mSystems.00072-19},
journal = {mSystems},
number = 2,
volume = 4,
place = {United States},
year = {2019},
month = {3}
}

Journal Article:
Free Publicly Available Full Text
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DOI: 10.1128/mSystems.00072-19

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