ParkinsonCanadaV1, Main, Exploration, bibRecord, 001D29

DETECT-a Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum

Identifieur interne : 001D29 ( Main/Exploration ); précédent : 001D28; suivant : 001D30

DETECT-a Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum

Auteurs : Stacy S. Hung [Canada] ; James Wasmuth [Canada] ; Christopher Sanford [Canada] ; John Parkinson [Canada]

Source :

Bioinformatics : (Oxford. Print) [ 1367-4803 ] ; 2010.

RBID : Pascal:10-0332015

Descripteurs français

Pascal (Inist)
- Plasmodium falciparum, Détection, Densité, Estimation, Enzyme, Classification, Application.
Wicri :
- topic : Enzyme, Classification.

English descriptors

KwdEn :
- Application, Classification, Density, Detection, Enzyme, Estimation, Plasmodium falciparum.

Abstract

Motivation: A major challenge in genomics is the accurate annotation of component genes. Enzymes are typically predicted using homology-based search methods, where the membership of a protein to an enzyme family is based on single-sequence comparisons. As such, these methods are often error-prone and lack useful measures of reliability for the prediction. Results: Here, we present DETECT, a probabilistic method for enzyme prediction that accounts for the sequence diversity across enzyme families. By comparing the global alignment scores of an unknown protein to those of all known enzymes, an integrated likelihood score can be readily calculated, ranking the reaction classes relevant for that protein. Comparisons to BLAST reveal significant improvements in enzyme annotation accuracy. Applied to Plasmodium falciparum, we identify potential annotation errors and predict novel enzymes of therapeutic interest. Availability: A standalone application is available from the website: http://www.compsysbio.org/projects/DETECT/ Contact: john.parkinson@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online.

Affiliations:

Links toward previous steps (curation, corpus...)

to stream PascalFrancis, to step Corpus: 000421
to stream PascalFrancis, to step Curation: 000856
to stream PascalFrancis, to step Checkpoint: 000374
to stream Main, to step Merge: 001E64
to stream Main, to step Curation: 001D29

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en" level="a">DETECT-a Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum</title>
<author><name sortKey="Hung, Stacy S" sort="Hung, Stacy S" uniqKey="Hung S" first="Stacy S." last="Hung">Stacy S. Hung</name>
<affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Program in Molecular Structure and Function, Hospital for Sick Children, 15-704 MaRS TMDT East, 101 College Street</s1>
<s2>Toronto, ON, M5G 1 L7</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>2 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>Toronto, ON, M5G 1 L7</wicri:noRegion>
</affiliation>
<affiliation wicri:level="4"><inist:fA14 i1="02"><s1>Department of Molecular Genetics, University of Toronto, Toronto, 1 Kings' College Circle</s1>
<s2>ON, M5S 1A8</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>ON, M5S 1A8</wicri:noRegion>
<orgName type="university">Université de Toronto</orgName>
<placeName><settlement type="city">Toronto</settlement>
<region type="state">Ontario</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wasmuth, James" sort="Wasmuth, James" uniqKey="Wasmuth J" first="James" last="Wasmuth">James Wasmuth</name>
<affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Program in Molecular Structure and Function, Hospital for Sick Children, 15-704 MaRS TMDT East, 101 College Street</s1>
<s2>Toronto, ON, M5G 1 L7</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>2 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>Toronto, ON, M5G 1 L7</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Sanford, Christopher" sort="Sanford, Christopher" uniqKey="Sanford C" first="Christopher" last="Sanford">Christopher Sanford</name>
<affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Program in Molecular Structure and Function, Hospital for Sick Children, 15-704 MaRS TMDT East, 101 College Street</s1>
<s2>Toronto, ON, M5G 1 L7</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>2 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>Toronto, ON, M5G 1 L7</wicri:noRegion>
</affiliation>
<affiliation wicri:level="4"><inist:fA14 i1="02"><s1>Department of Molecular Genetics, University of Toronto, Toronto, 1 Kings' College Circle</s1>
<s2>ON, M5S 1A8</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>ON, M5S 1A8</wicri:noRegion>
<orgName type="university">Université de Toronto</orgName>
<placeName><settlement type="city">Toronto</settlement>
<region type="state">Ontario</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name>
<affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Program in Molecular Structure and Function, Hospital for Sick Children, 15-704 MaRS TMDT East, 101 College Street</s1>
<s2>Toronto, ON, M5G 1 L7</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>2 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>Toronto, ON, M5G 1 L7</wicri:noRegion>
</affiliation>
<affiliation wicri:level="4"><inist:fA14 i1="02"><s1>Department of Molecular Genetics, University of Toronto, Toronto, 1 Kings' College Circle</s1>
<s2>ON, M5S 1A8</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>ON, M5S 1A8</wicri:noRegion>
<orgName type="university">Université de Toronto</orgName>
<placeName><settlement type="city">Toronto</settlement>
<region type="state">Ontario</region>
</placeName>
</affiliation>
<affiliation wicri:level="4"><inist:fA14 i1="03"><s1>Department of Biochemistry, University of Toronto, Toronto, 1 Kings' College Circle</s1>
<s2>ON, M5S 1A8</s2>
<s3>CAN</s3>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>ON, M5S 1A8</wicri:noRegion>
<orgName type="university">Université de Toronto</orgName>
<placeName><settlement type="city">Toronto</settlement>
<region type="state">Ontario</region>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">INIST</idno>
<idno type="inist">10-0332015</idno>
<date when="2010">2010</date>
<idno type="stanalyst">PASCAL 10-0332015 INIST</idno>
<idno type="RBID">Pascal:10-0332015</idno>
<idno type="wicri:Area/PascalFrancis/Corpus">000421</idno>
<idno type="wicri:Area/PascalFrancis/Curation">000856</idno>
<idno type="wicri:Area/PascalFrancis/Checkpoint">000374</idno>
<idno type="wicri:explorRef" wicri:stream="PascalFrancis" wicri:step="Checkpoint">000374</idno>
<idno type="wicri:doubleKey">1367-4803:2010:Hung S:detect:a:density</idno>
<idno type="wicri:Area/Main/Merge">001E64</idno>
<idno type="wicri:Area/Main/Curation">001D29</idno>
<idno type="wicri:Area/Main/Exploration">001D29</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a">DETECT-a Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum</title>
<author><name sortKey="Hung, Stacy S" sort="Hung, Stacy S" uniqKey="Hung S" first="Stacy S." last="Hung">Stacy S. Hung</name>
<affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Program in Molecular Structure and Function, Hospital for Sick Children, 15-704 MaRS TMDT East, 101 College Street</s1>
<s2>Toronto, ON, M5G 1 L7</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>2 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>Toronto, ON, M5G 1 L7</wicri:noRegion>
</affiliation>
<affiliation wicri:level="4"><inist:fA14 i1="02"><s1>Department of Molecular Genetics, University of Toronto, Toronto, 1 Kings' College Circle</s1>
<s2>ON, M5S 1A8</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>ON, M5S 1A8</wicri:noRegion>
<orgName type="university">Université de Toronto</orgName>
<placeName><settlement type="city">Toronto</settlement>
<region type="state">Ontario</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Wasmuth, James" sort="Wasmuth, James" uniqKey="Wasmuth J" first="James" last="Wasmuth">James Wasmuth</name>
<affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Program in Molecular Structure and Function, Hospital for Sick Children, 15-704 MaRS TMDT East, 101 College Street</s1>
<s2>Toronto, ON, M5G 1 L7</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>2 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>Toronto, ON, M5G 1 L7</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Sanford, Christopher" sort="Sanford, Christopher" uniqKey="Sanford C" first="Christopher" last="Sanford">Christopher Sanford</name>
<affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Program in Molecular Structure and Function, Hospital for Sick Children, 15-704 MaRS TMDT East, 101 College Street</s1>
<s2>Toronto, ON, M5G 1 L7</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>2 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>Toronto, ON, M5G 1 L7</wicri:noRegion>
</affiliation>
<affiliation wicri:level="4"><inist:fA14 i1="02"><s1>Department of Molecular Genetics, University of Toronto, Toronto, 1 Kings' College Circle</s1>
<s2>ON, M5S 1A8</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>ON, M5S 1A8</wicri:noRegion>
<orgName type="university">Université de Toronto</orgName>
<placeName><settlement type="city">Toronto</settlement>
<region type="state">Ontario</region>
</placeName>
</affiliation>
</author>
<author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name>
<affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Program in Molecular Structure and Function, Hospital for Sick Children, 15-704 MaRS TMDT East, 101 College Street</s1>
<s2>Toronto, ON, M5G 1 L7</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>2 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>Toronto, ON, M5G 1 L7</wicri:noRegion>
</affiliation>
<affiliation wicri:level="4"><inist:fA14 i1="02"><s1>Department of Molecular Genetics, University of Toronto, Toronto, 1 Kings' College Circle</s1>
<s2>ON, M5S 1A8</s2>
<s3>CAN</s3>
<sZ>1 aut.</sZ>
<sZ>3 aut.</sZ>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>ON, M5S 1A8</wicri:noRegion>
<orgName type="university">Université de Toronto</orgName>
<placeName><settlement type="city">Toronto</settlement>
<region type="state">Ontario</region>
</placeName>
</affiliation>
<affiliation wicri:level="4"><inist:fA14 i1="03"><s1>Department of Biochemistry, University of Toronto, Toronto, 1 Kings' College Circle</s1>
<s2>ON, M5S 1A8</s2>
<s3>CAN</s3>
<sZ>4 aut.</sZ>
</inist:fA14>
<country>Canada</country>
<wicri:noRegion>ON, M5S 1A8</wicri:noRegion>
<orgName type="university">Université de Toronto</orgName>
<placeName><settlement type="city">Toronto</settlement>
<region type="state">Ontario</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j" type="main">Bioinformatics : (Oxford. Print)</title>
<title level="j" type="abbreviated">Bioinformatics : (Oxf., Print)</title>
<idno type="ISSN">1367-4803</idno>
<imprint><date when="2010">2010</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
<seriesStmt><title level="j" type="main">Bioinformatics : (Oxford. Print)</title>
<title level="j" type="abbreviated">Bioinformatics : (Oxf., Print)</title>
<idno type="ISSN">1367-4803</idno>
</seriesStmt>
</fileDesc>
<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Application</term>
<term>Classification</term>
<term>Density</term>
<term>Detection</term>
<term>Enzyme</term>
<term>Estimation</term>
<term>Plasmodium falciparum</term>
</keywords>
<keywords scheme="Pascal" xml:lang="fr"><term>Plasmodium falciparum</term>
<term>Détection</term>
<term>Densité</term>
<term>Estimation</term>
<term>Enzyme</term>
<term>Classification</term>
<term>Application</term>
</keywords>
<keywords scheme="Wicri" type="topic" xml:lang="fr"><term>Enzyme</term>
<term>Classification</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en">Motivation: A major challenge in genomics is the accurate annotation of component genes. Enzymes are typically predicted using homology-based search methods, where the membership of a protein to an enzyme family is based on single-sequence comparisons. As such, these methods are often error-prone and lack useful measures of reliability for the prediction. Results: Here, we present DETECT, a probabilistic method for enzyme prediction that accounts for the sequence diversity across enzyme families. By comparing the global alignment scores of an unknown protein to those of all known enzymes, an integrated likelihood score can be readily calculated, ranking the reaction classes relevant for that protein. Comparisons to BLAST reveal significant improvements in enzyme annotation accuracy. Applied to Plasmodium falciparum, we identify potential annotation errors and predict novel enzymes of therapeutic interest. Availability: A standalone application is available from the website: http://www.compsysbio.org/projects/DETECT/ Contact: john.parkinson@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online.</div>
</front>
</TEI>
<affiliations><list><country><li>Canada</li>
</country>
<region><li>Ontario</li>
</region>
<settlement><li>Toronto</li>
</settlement>
<orgName><li>Université de Toronto</li>
</orgName>
</list>
<tree><country name="Canada"><noRegion><name sortKey="Hung, Stacy S" sort="Hung, Stacy S" uniqKey="Hung S" first="Stacy S." last="Hung">Stacy S. Hung</name>
</noRegion>
<name sortKey="Hung, Stacy S" sort="Hung, Stacy S" uniqKey="Hung S" first="Stacy S." last="Hung">Stacy S. Hung</name>
<name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name>
<name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name>
<name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name>
<name sortKey="Sanford, Christopher" sort="Sanford, Christopher" uniqKey="Sanford C" first="Christopher" last="Sanford">Christopher Sanford</name>
<name sortKey="Sanford, Christopher" sort="Sanford, Christopher" uniqKey="Sanford C" first="Christopher" last="Sanford">Christopher Sanford</name>
<name sortKey="Wasmuth, James" sort="Wasmuth, James" uniqKey="Wasmuth J" first="James" last="Wasmuth">James Wasmuth</name>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Wicri/Canada/explor/ParkinsonCanadaV1/Data/Main/Exploration

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001D29 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 001D29 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Wicri/Canada
   |area=    ParkinsonCanadaV1
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     Pascal:10-0332015
   |texte=   DETECT-a Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum
}}

This area was generated with Dilib version V0.6.29.
Data generation: Thu May 4 22:20:19 2017. Site generation: Fri Dec 23 23:17:26 2022

	La maladie de Parkinson au Canada (serveur d'exploration)
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.

La maladie de Parkinson au Canada (serveur d'exploration)

DETECT-a Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum

DETECT-a Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri