Federal University of Mato Grosso do Sul Xanthomonas arboricola Project College of Computing - UFMS

HGT Analysis

Alien Hunter (AH) (Vernikos & Parkhill 2006) has been used to find anomalous regions and horizontal transfer candidates. AH identifies regions that may have been laterally transferred by finding regions with unusual sequence composition in terms of k-mers for various values of k (called interpolated variable order motifs).

An anomalous region has AH score greater than an automatically calculated threshold that takes into account the sequence composition of the whole genome (the background composition).

AH was run on 5 X. arboricola pv. juglandis genomes. The table below presents, for each genome (the concatenation of all contigs), a plot showing AH anomalous regions, and also a list of genes inside these regions. Each listed gene comes with the genomes, if any, where its homologs are, given by OrthoMCL (Li et al.2003).

Results by genome

StrainAlien
Hunter
plot		Genes
in AH
regions
Xarjug_Xaj417pdfhgts
Xar_3004pdfhgts
Xarcelebensis_NCPP1832pdfhgts
Xarcelebensis_NCPPB1630pdfhgts
Xar_CFBP7634pdfhgts
Xar_CFBP7651pdfhgts
Xar_CITA124pdfhgts
Xar_CITA14pdfhgts
Xar_CITA44pdfhgts
Xarcorylina_NCCB100457pdfhgts
Xarjug_CFBP2528pdfhgts
Xarjug_CFBP7179pdfhgts
Xarjug_J303pdfhgts
Xarjug_NCPPB1447pdfhgts
Xarpruni_CFBP3894pdfhgts
Xarpruni_IVIA2626pdfhgts
Xarpruni_MAFF301420pdfhgts
Xarpruni_MAFF301427pdfhgts
Xarpruni_MAFF311562pdfhgts
Xarpruni_Xap33pdfhgts

References


Funding

CAPES

CNPq Fundect