Eintrag weiter verarbeiten
Evolutionary analysis of enzymes using Chisel
Gespeichert in:
| Zeitschriftentitel: | Bioinformatics |
|---|---|
| Personen und Körperschaften: | , , , , |
| In: | Bioinformatics, 23, 2007, 22, S. 2961-2968 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Oxford University Press (OUP)
|
| Schlagwörter: |
| author_facet |
Rodriguez, Alexis A. Bompada, Tanuja Syed, Mustafa Shah, Parantu K. Maltsev, Natalia Rodriguez, Alexis A. Bompada, Tanuja Syed, Mustafa Shah, Parantu K. Maltsev, Natalia |
|---|---|
| author |
Rodriguez, Alexis A. Bompada, Tanuja Syed, Mustafa Shah, Parantu K. Maltsev, Natalia |
| spellingShingle |
Rodriguez, Alexis A. Bompada, Tanuja Syed, Mustafa Shah, Parantu K. Maltsev, Natalia Bioinformatics Evolutionary analysis of enzymes using Chisel Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| author_sort |
rodriguez, alexis a. |
| spelling |
Rodriguez, Alexis A. Bompada, Tanuja Syed, Mustafa Shah, Parantu K. Maltsev, Natalia 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/btm421 <jats:title>Abstract</jats:title><jats:p>Motivation: Availability of large volumes of genomic and enzymatic data for taxonomically and phenotypically diverse organisms allows for exploration of the adaptive mechanisms that led to diversification of enzymatic functions. We present Chisel, a computational framework and a pipeline for an automated, high-resolution analysis of evolutionary variations of enzymes. Chisel allows automatic as well as interactive identification, and characterization of enzymatic sequences. Such knowledge can be utilized for comparative genomics, microbial diagnostics, metabolic engineering, drug design and analysis of metagenomes.</jats:p><jats:p>Results: Chisel is a comprehensive resource that contains 8575 clusters and subsequent computational models specific for 939 distinct enzymatic functions and, when data is sufficient, their taxonomic variations. Application of Chisel to identification of enzymatic sequences in newly sequenced genomes, analysis of organism-specific metabolic networks, ‘binning’ of metagenomes and other biological problems are presented. We also provide a thorough analysis of Chisel performance with other similar resources and manual annotations on Shewanella oneidensis MR1 genome.</jats:p><jats:p>Availability: Chisel is available for interactive use at http://compbio.mcs.anl.gov/CHISEL. The website also provides a user manual, clusters and function-specific computational models.</jats:p><jats:p>Contact: arodri7@mcs.anl.gov or maltsev@mcs.anl.gov</jats:p><jats:p>Supplementary information: Additional data can be found at http://compbio.mcs.anl.gov/CHISEL/htmls/refs.html</jats:p> Evolutionary analysis of enzymes using Chisel Bioinformatics |
| doi_str_mv |
10.1093/bioinformatics/btm421 |
| facet_avail |
Online Free |
| finc_class_facet |
Chemie und Pharmazie Mathematik Informatik Biologie |
| format |
ElectronicArticle |
| fullrecord |
blob:ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9iaW9pbmZvcm1hdGljcy9idG00MjE |
| id |
ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9iaW9pbmZvcm1hdGljcy9idG00MjE |
| institution |
DE-Gla1 DE-Zi4 DE-15 DE-Pl11 DE-Rs1 DE-105 DE-14 DE-Ch1 DE-L229 DE-D275 DE-Bn3 DE-Brt1 DE-Zwi2 DE-D161 |
| imprint |
Oxford University Press (OUP), 2007 |
| imprint_str_mv |
Oxford University Press (OUP), 2007 |
| issn |
1367-4811 1367-4803 |
| issn_str_mv |
1367-4811 1367-4803 |
| language |
English |
| mega_collection |
Oxford University Press (OUP) (CrossRef) |
| match_str |
rodriguez2007evolutionaryanalysisofenzymesusingchisel |
| publishDateSort |
2007 |
| publisher |
Oxford University Press (OUP) |
| recordtype |
ai |
| record_format |
ai |
| series |
Bioinformatics |
| source_id |
49 |
| title |
Evolutionary analysis of enzymes using Chisel |
| title_unstemmed |
Evolutionary analysis of enzymes using Chisel |
| title_full |
Evolutionary analysis of enzymes using Chisel |
| title_fullStr |
Evolutionary analysis of enzymes using Chisel |
| title_full_unstemmed |
Evolutionary analysis of enzymes using Chisel |
| title_short |
Evolutionary analysis of enzymes using Chisel |
| title_sort |
evolutionary analysis of enzymes using chisel |
| topic |
Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| url |
http://dx.doi.org/10.1093/bioinformatics/btm421 |
| publishDate |
2007 |
| physical |
2961-2968 |
| description |
<jats:title>Abstract</jats:title><jats:p>Motivation: Availability of large volumes of genomic and enzymatic data for taxonomically and phenotypically diverse organisms allows for exploration of the adaptive mechanisms that led to diversification of enzymatic functions. We present Chisel, a computational framework and a pipeline for an automated, high-resolution analysis of evolutionary variations of enzymes. Chisel allows automatic as well as interactive identification, and characterization of enzymatic sequences. Such knowledge can be utilized for comparative genomics, microbial diagnostics, metabolic engineering, drug design and analysis of metagenomes.</jats:p><jats:p>Results: Chisel is a comprehensive resource that contains 8575 clusters and subsequent computational models specific for 939 distinct enzymatic functions and, when data is sufficient, their taxonomic variations. Application of Chisel to identification of enzymatic sequences in newly sequenced genomes, analysis of organism-specific metabolic networks, ‘binning’ of metagenomes and other biological problems are presented. We also provide a thorough analysis of Chisel performance with other similar resources and manual annotations on Shewanella oneidensis MR1 genome.</jats:p><jats:p>Availability: Chisel is available for interactive use at http://compbio.mcs.anl.gov/CHISEL. The website also provides a user manual, clusters and function-specific computational models.</jats:p><jats:p>Contact: arodri7@mcs.anl.gov or maltsev@mcs.anl.gov</jats:p><jats:p>Supplementary information: Additional data can be found at http://compbio.mcs.anl.gov/CHISEL/htmls/refs.html</jats:p> |
| container_issue |
22 |
| container_start_page |
2961 |
| container_title |
Bioinformatics |
| container_volume |
23 |
| format_de105 |
Article, E-Article |
| format_de14 |
Article, E-Article |
| format_de15 |
Article, E-Article |
| format_de520 |
Article, E-Article |
| format_de540 |
Article, E-Article |
| format_dech1 |
Article, E-Article |
| format_ded117 |
Article, E-Article |
| format_degla1 |
E-Article |
| format_del152 |
Buch |
| format_del189 |
Article, E-Article |
| format_dezi4 |
Article |
| format_dezwi2 |
Article, E-Article |
| format_finc |
Article, E-Article |
| format_nrw |
Article, E-Article |
| _version_ |
1792331074881191948 |
| geogr_code |
not assigned |
| last_indexed |
2024-03-01T13:35:09.491Z |
| geogr_code_person |
not assigned |
| openURL |
url_ver=Z39.88-2004&ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fvufind.svn.sourceforge.net%3Agenerator&rft.title=Evolutionary+analysis+of+enzymes+using+Chisel&rft.date=2007-11-15&genre=article&issn=1367-4803&volume=23&issue=22&spage=2961&epage=2968&pages=2961-2968&jtitle=Bioinformatics&atitle=Evolutionary+analysis+of+enzymes+using+Chisel&aulast=Maltsev&aufirst=Natalia&rft_id=info%3Adoi%2F10.1093%2Fbioinformatics%2Fbtm421&rft.language%5B0%5D=eng |
| SOLR | |
| _version_ | 1792331074881191948 |
| author | Rodriguez, Alexis A., Bompada, Tanuja, Syed, Mustafa, Shah, Parantu K., Maltsev, Natalia |
| author_facet | Rodriguez, Alexis A., Bompada, Tanuja, Syed, Mustafa, Shah, Parantu K., Maltsev, Natalia, Rodriguez, Alexis A., Bompada, Tanuja, Syed, Mustafa, Shah, Parantu K., Maltsev, Natalia |
| author_sort | rodriguez, alexis a. |
| container_issue | 22 |
| container_start_page | 2961 |
| container_title | Bioinformatics |
| container_volume | 23 |
| description | <jats:title>Abstract</jats:title><jats:p>Motivation: Availability of large volumes of genomic and enzymatic data for taxonomically and phenotypically diverse organisms allows for exploration of the adaptive mechanisms that led to diversification of enzymatic functions. We present Chisel, a computational framework and a pipeline for an automated, high-resolution analysis of evolutionary variations of enzymes. Chisel allows automatic as well as interactive identification, and characterization of enzymatic sequences. Such knowledge can be utilized for comparative genomics, microbial diagnostics, metabolic engineering, drug design and analysis of metagenomes.</jats:p><jats:p>Results: Chisel is a comprehensive resource that contains 8575 clusters and subsequent computational models specific for 939 distinct enzymatic functions and, when data is sufficient, their taxonomic variations. Application of Chisel to identification of enzymatic sequences in newly sequenced genomes, analysis of organism-specific metabolic networks, ‘binning’ of metagenomes and other biological problems are presented. We also provide a thorough analysis of Chisel performance with other similar resources and manual annotations on Shewanella oneidensis MR1 genome.</jats:p><jats:p>Availability: Chisel is available for interactive use at http://compbio.mcs.anl.gov/CHISEL. The website also provides a user manual, clusters and function-specific computational models.</jats:p><jats:p>Contact: arodri7@mcs.anl.gov or maltsev@mcs.anl.gov</jats:p><jats:p>Supplementary information: Additional data can be found at http://compbio.mcs.anl.gov/CHISEL/htmls/refs.html</jats:p> |
| doi_str_mv | 10.1093/bioinformatics/btm421 |
| facet_avail | Online, Free |
| finc_class_facet | Chemie und Pharmazie, Mathematik, Informatik, Biologie |
| format | ElectronicArticle |
| format_de105 | Article, E-Article |
| format_de14 | Article, E-Article |
| format_de15 | Article, E-Article |
| format_de520 | Article, E-Article |
| format_de540 | Article, E-Article |
| format_dech1 | Article, E-Article |
| format_ded117 | Article, E-Article |
| format_degla1 | E-Article |
| format_del152 | Buch |
| format_del189 | Article, E-Article |
| format_dezi4 | Article |
| format_dezwi2 | Article, E-Article |
| format_finc | Article, E-Article |
| format_nrw | Article, E-Article |
| geogr_code | not assigned |
| geogr_code_person | not assigned |
| id | ai-49-aHR0cDovL2R4LmRvaS5vcmcvMTAuMTA5My9iaW9pbmZvcm1hdGljcy9idG00MjE |
| imprint | Oxford University Press (OUP), 2007 |
| imprint_str_mv | Oxford University Press (OUP), 2007 |
| institution | DE-Gla1, DE-Zi4, DE-15, DE-Pl11, DE-Rs1, DE-105, DE-14, DE-Ch1, DE-L229, DE-D275, DE-Bn3, DE-Brt1, DE-Zwi2, DE-D161 |
| issn | 1367-4811, 1367-4803 |
| issn_str_mv | 1367-4811, 1367-4803 |
| language | English |
| last_indexed | 2024-03-01T13:35:09.491Z |
| match_str | rodriguez2007evolutionaryanalysisofenzymesusingchisel |
| mega_collection | Oxford University Press (OUP) (CrossRef) |
| physical | 2961-2968 |
| publishDate | 2007 |
| publishDateSort | 2007 |
| publisher | Oxford University Press (OUP) |
| record_format | ai |
| recordtype | ai |
| series | Bioinformatics |
| source_id | 49 |
| spelling | Rodriguez, Alexis A. Bompada, Tanuja Syed, Mustafa Shah, Parantu K. Maltsev, Natalia 1367-4811 1367-4803 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/btm421 <jats:title>Abstract</jats:title><jats:p>Motivation: Availability of large volumes of genomic and enzymatic data for taxonomically and phenotypically diverse organisms allows for exploration of the adaptive mechanisms that led to diversification of enzymatic functions. We present Chisel, a computational framework and a pipeline for an automated, high-resolution analysis of evolutionary variations of enzymes. Chisel allows automatic as well as interactive identification, and characterization of enzymatic sequences. Such knowledge can be utilized for comparative genomics, microbial diagnostics, metabolic engineering, drug design and analysis of metagenomes.</jats:p><jats:p>Results: Chisel is a comprehensive resource that contains 8575 clusters and subsequent computational models specific for 939 distinct enzymatic functions and, when data is sufficient, their taxonomic variations. Application of Chisel to identification of enzymatic sequences in newly sequenced genomes, analysis of organism-specific metabolic networks, ‘binning’ of metagenomes and other biological problems are presented. We also provide a thorough analysis of Chisel performance with other similar resources and manual annotations on Shewanella oneidensis MR1 genome.</jats:p><jats:p>Availability: Chisel is available for interactive use at http://compbio.mcs.anl.gov/CHISEL. The website also provides a user manual, clusters and function-specific computational models.</jats:p><jats:p>Contact: arodri7@mcs.anl.gov or maltsev@mcs.anl.gov</jats:p><jats:p>Supplementary information: Additional data can be found at http://compbio.mcs.anl.gov/CHISEL/htmls/refs.html</jats:p> Evolutionary analysis of enzymes using Chisel Bioinformatics |
| spellingShingle | Rodriguez, Alexis A., Bompada, Tanuja, Syed, Mustafa, Shah, Parantu K., Maltsev, Natalia, Bioinformatics, Evolutionary analysis of enzymes using Chisel, Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| title | Evolutionary analysis of enzymes using Chisel |
| title_full | Evolutionary analysis of enzymes using Chisel |
| title_fullStr | Evolutionary analysis of enzymes using Chisel |
| title_full_unstemmed | Evolutionary analysis of enzymes using Chisel |
| title_short | Evolutionary analysis of enzymes using Chisel |
| title_sort | evolutionary analysis of enzymes using chisel |
| title_unstemmed | Evolutionary analysis of enzymes using Chisel |
| topic | Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| url | http://dx.doi.org/10.1093/bioinformatics/btm421 |