Inferring Horizontal Gene Transfer with DarkHorse, Phylomizer, and ETE Toolkits
Por:
Delaye L., Vargas C., Latorre A., Moya A.
Publicada:
1 ene 2020
Resumen:
In this chapter, we describe how to use DarkHorse2.0 to search for xenologs in the genome of the cyanobacterium Synechococcus elongatus PCC 7942. DarkHorse is an implicit phylogenetic method that uses BLAST searches to identify proteins having close homologs of unexpected taxonomic affiliation. Once a set of putative xenologs are identified, Phylomizer is used to reconstruct phylogenetic trees. Phylomizer reproduces all the necessary steps to perform a basic phylogenetic analysis. The combined use of DarkHorse and Phylomizer allows the identification of genes incorporated into a given genome by HGT. © Springer Science+Business Media, LLC, part of Springer Nature 2020.
Filiaciones:
Delaye L.:
Departamento de Ingeniería Genética, CINVESTAV Irapuato, Irapuato, Guanajuato, Mexico
Vargas C.:
Institute of Integrative Systems Biology, University of València and CSIC, València, Spain
Latorre A.:
Institute of Integrative Systems Biology, University of València and CSIC, València, Spain
Joint Unit in Genomics and Health, FISABIO-Public Health – I2Sysbio, University of Valencia and CSIC, València, Spain
CIBER in Epidemiology and Public Health, Madrid, Spain
Moya A.:
Institute of Integrative Systems Biology, University of València and CSIC, València, Spain
Joint Unit in Genomics and Health, FISABIO-Public Health – I2Sysbio, University of Valencia and CSIC, València, Spain
CIBER in Epidemiology and Public Health, Madrid, Spain
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