EvoMining specifications

Information


Unique identifier OMICS_17095
Name EvoMining
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Maintainer


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Publication for EvoMining

EvoMining in publications

 (6)
PMCID: 5801464
PMID: 29437921
DOI: 10.1128/mBio.02283-17

[…] all genomes were retrieved from genbank, reannotated with rast () to ensure consistency of annotation across the database, and then analyzed in a bespoke bioinformatics pipeline based on evomining (, ) (see fig. s1 and table s1 at https://doi.org/10.6084/m9.figshare.5772963.v1). it was hypothesized that, if precursor-supplying pathways are a contributing factor to the adaptive […]

PMCID: 5702503
PMID: 29209209
DOI: 10.3389/fphar.2017.00828

[…] focuses on the identification of new bgc types by applying three approaches; namely pattern-based mining, phylogenetic mining and comparative genomic mining. these further include cluster finder, evomining, and algorithim, respectively. tools for identification of bgcs with respect to metagenomes include pcr-based sequence-tag and the shotgun assembly approach. the sequence-tag approach […]

PMCID: 5618411
PMID: 28846659
DOI: 10.3390/md15090272

[…] and post-translationally modified peptides (ripps) and terpene products and has been expanded from bgc mining in bacteria and fungi to bgc mining in plants []. another recently developed tool is evomining, which integrates evolutionary concepts related to the emergence of natural product biosynthesis into genome mining. it is a newly developed phylogenomics approach toward bgc analysis […]

PMCID: 4993170
PMID: 27470984
DOI: 10.1111/1751-7915.12388

[…] bacterial genomes and detected about 30 000 putative biosynthetic gene clusters. another method that addresses the problem of finding novel pathways is based on evolutionary distances and was called evomining (cruz‐morales et al., ). evomining is based on the assumption that most enzymes used in secondary metabolism have been duplicated and evolved from primary metabolism (cruz‐morales et al., […]

PMCID: 4748306
PMID: 26904093
DOI: 10.3389/fgene.2016.00004

[…] et al. developed a functional phylogenomics platform to identify expanded, repurposed enzyme families, which have been recruited from central metabolism into the context of specialized metabolism. evomining uses single-gene topologies to reveal characteristic phylogenetic signatures of rapid evolution that can be further analyzed in detail with the construction of hidden markov models (hmm) […]


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EvoMining institution(s)
Evolution of Metabolic Diversity Laboratory, Langebio, Cinvestav-IPN, Irapuato, Guanajuato, Mexico; Trace Element Speciation Laboratory (TESLA) College of Physical Sciences, Aberdeen, Scotland, UK
EvoMining funding source(s)
Funded by Conacyt Mexico (Grant nos. 179290 and 177568) and FINNOVA Mexico (Grant no. 214716), Conacyt scholarship (No. 28830), Cinvestav posdoctoral fellowship, and the College of Physical Sciences, University of Aberdeen, UK.

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