KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
Abstract Summary KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being co...
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| Vydané v: | Bioinformatics Ročník 36; číslo 7; s. 2251 - 2252 |
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| Hlavní autori: | , , , , , , |
| Médium: | Journal Article |
| Jazyk: | English |
| Vydavateľské údaje: |
England
Oxford University Press
01.04.2020
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| Predmet: | |
| ISSN: | 1367-4803, 1367-4811, 1460-2059, 1367-4811 |
| On-line prístup: | Získať plný text |
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| Abstract | Abstract
Summary
KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being comparable to the best performing tools. Function annotation by KofamKOALA helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction.
Availability and implementation
KofamKOALA, KofamScan and KOfam are freely available from GenomeNet (https://www.genome.jp/tools/kofamkoala/).
Supplementary information
Supplementary data are available at Bioinformatics online. |
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| AbstractList | KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being comparable to the best performing tools. Function annotation by KofamKOALA helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction.SUMMARYKofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being comparable to the best performing tools. Function annotation by KofamKOALA helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction.KofamKOALA, KofamScan and KOfam are freely available from GenomeNet (https://www.genome.jp/tools/kofamkoala/).AVAILABILITY AND IMPLEMENTATIONKofamKOALA, KofamScan and KOfam are freely available from GenomeNet (https://www.genome.jp/tools/kofamkoala/).Supplementary data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being comparable to the best performing tools. Function annotation by KofamKOALA helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction. KofamKOALA, KofamScan and KOfam are freely available from GenomeNet (https://www.genome.jp/tools/kofamkoala/). Supplementary data are available at Bioinformatics online. Abstract Summary KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam) with pre-computed adaptive score thresholds. KofamKOALA is faster than existing KO assignment tools with its accuracy being comparable to the best performing tools. Function annotation by KofamKOALA helps linking genes to KEGG resources such as the KEGG pathway maps and facilitates molecular network reconstruction. Availability and implementation KofamKOALA, KofamScan and KOfam are freely available from GenomeNet (https://www.genome.jp/tools/kofamkoala/). Supplementary information Supplementary data are available at Bioinformatics online. |
| Author | Endo, Hisashi Goto, Susumu Ogata, Hiroyuki Blanc-Mathieu, Romain Aramaki, Takuya Ohkubo, Koichi Kanehisa, Minoru |
| AuthorAffiliation | 2 Hewlett-Packard Japan Ltd. , Koto-ku, Tokyo 136-8711 1 Bioinformatics Center, Institute for Chemical Research, Kyoto University , Gokasho, Uji, Kyoto 611-0011 3 Database Center for Life Science, Research Organization of Information and Systems , Kashiwa, Chiba 277-0871, Japan |
| AuthorAffiliation_xml | – name: 1 Bioinformatics Center, Institute for Chemical Research, Kyoto University , Gokasho, Uji, Kyoto 611-0011 – name: 3 Database Center for Life Science, Research Organization of Information and Systems , Kashiwa, Chiba 277-0871, Japan – name: 2 Hewlett-Packard Japan Ltd. , Koto-ku, Tokyo 136-8711 |
| Author_xml | – sequence: 1 givenname: Takuya surname: Aramaki fullname: Aramaki, Takuya organization: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 – sequence: 2 givenname: Romain surname: Blanc-Mathieu fullname: Blanc-Mathieu, Romain organization: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 – sequence: 3 givenname: Hisashi surname: Endo fullname: Endo, Hisashi organization: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 – sequence: 4 givenname: Koichi surname: Ohkubo fullname: Ohkubo, Koichi organization: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 – sequence: 5 givenname: Minoru surname: Kanehisa fullname: Kanehisa, Minoru organization: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 – sequence: 6 givenname: Susumu surname: Goto fullname: Goto, Susumu organization: Database Center for Life Science, Research Organization of Information and Systems, Kashiwa, Chiba 277-0871, Japan – sequence: 7 givenname: Hiroyuki surname: Ogata fullname: Ogata, Hiroyuki email: ogata@kuicr.kyoto-u.ac.jp organization: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31742321$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1371/journal.pone.0103833 10.1093/nar/gki198 10.1371/journal.pcbi.1000069 10.1093/nar/28.1.27 10.1093/nar/gkm321 10.1093/nar/25.17.3389 10.1093/bioinformatics/bts565 10.1016/j.jmb.2015.11.006 |
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| Copyright | The Author(s) 2019. Published by Oxford University Press. 2019 The Author(s) 2019. Published by Oxford University Press. |
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| References | Katoh (2023062300073444800_btz859-B6) 2005; 33 Fu (2023062300073444800_btz859-B3) 2012; 28 Moriya (2023062300073444800_btz859-B7) 2007; 35 Altschul (2023062300073444800_btz859-B1) 1997; 25 Eddy (2023062300073444800_btz859-B2) 2008; 4 Kanehisa (2023062300073444800_btz859-B5) 2016; 428 Suzuki (2023062300073444800_btz859-B8) 2014; 9 Kanehisa (2023062300073444800_btz859-B4) 2000; 28 |
| References_xml | – volume: 9 start-page: e103833 year: 2014 ident: 2023062300073444800_btz859-B8 article-title: GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array publication-title: PLoS One doi: 10.1371/journal.pone.0103833 – volume: 33 start-page: 511 year: 2005 ident: 2023062300073444800_btz859-B6 article-title: MAFFT version 5: improvement in accuracy of multiple sequence alignment publication-title: Nucleic Acids Res doi: 10.1093/nar/gki198 – volume: 4 start-page: e1000069 year: 2008 ident: 2023062300073444800_btz859-B2 article-title: A probabilistic model of local sequence alignment that simplifies statistical significance estimation publication-title: PLoS Comput. Biol doi: 10.1371/journal.pcbi.1000069 – volume: 28 start-page: 27 year: 2000 ident: 2023062300073444800_btz859-B4 article-title: KEGG: Kyoto encyclopedia of genes and genomes publication-title: Nucleic Acids Res doi: 10.1093/nar/28.1.27 – volume: 35 start-page: W182 year: 2007 ident: 2023062300073444800_btz859-B7 article-title: KAAS: an automatic genome annotation and pathway reconstruction server publication-title: Nucleic Acids Res doi: 10.1093/nar/gkm321 – volume: 25 start-page: 3389 year: 1997 ident: 2023062300073444800_btz859-B1 article-title: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs publication-title: Nucleic Acids Res doi: 10.1093/nar/25.17.3389 – volume: 28 start-page: 3150 year: 2012 ident: 2023062300073444800_btz859-B3 article-title: CD-HIT: accelerated for clustering the next-generation sequencing data publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts565 – volume: 428 start-page: 726 year: 2016 ident: 2023062300073444800_btz859-B5 article-title: BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences publication-title: J. Mol. Biol doi: 10.1016/j.jmb.2015.11.006 |
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Summary
KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov... KofamKOALA is a web server to assign KEGG Orthologs (KOs) to protein sequences by homology search against a database of profile hidden Markov models (KOfam)... |
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| Title | KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold |
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