KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold

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...

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Autores principales: Aramaki, Takuya, Blanc-Mathieu, Romain, Endo, Hisashi, Ohkubo, Koichi, Kanehisa, Minoru, Goto, Susumu, Ogata, Hiroyuki
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7141845/
https://www.ncbi.nlm.nih.gov/pubmed/31742321
http://dx.doi.org/10.1093/bioinformatics/btz859
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author Aramaki, Takuya
Blanc-Mathieu, Romain
Endo, Hisashi
Ohkubo, Koichi
Kanehisa, Minoru
Goto, Susumu
Ogata, Hiroyuki
author_facet Aramaki, Takuya
Blanc-Mathieu, Romain
Endo, Hisashi
Ohkubo, Koichi
Kanehisa, Minoru
Goto, Susumu
Ogata, Hiroyuki
author_sort Aramaki, Takuya
collection PubMed
description 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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spelling pubmed-71418452020-04-13 KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold Aramaki, Takuya Blanc-Mathieu, Romain Endo, Hisashi Ohkubo, Koichi Kanehisa, Minoru Goto, Susumu Ogata, Hiroyuki Bioinformatics Applications Notes 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. Oxford University Press 2020-04-01 2019-11-19 /pmc/articles/PMC7141845/ /pubmed/31742321 http://dx.doi.org/10.1093/bioinformatics/btz859 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Aramaki, Takuya
Blanc-Mathieu, Romain
Endo, Hisashi
Ohkubo, Koichi
Kanehisa, Minoru
Goto, Susumu
Ogata, Hiroyuki
KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
title KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
title_full KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
title_fullStr KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
title_full_unstemmed KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
title_short KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
title_sort kofamkoala: kegg ortholog assignment based on profile hmm and adaptive score threshold
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7141845/
https://www.ncbi.nlm.nih.gov/pubmed/31742321
http://dx.doi.org/10.1093/bioinformatics/btz859
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