Federal University of Mato Grosso do Sul BIGA Serratia 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 Alcaligenes genomes and one Achromobacter arsenitoxydans. 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
S_ufop_01pdfhgts
S_ficaria_NBRC102596pdfhgts
S_fonticola_DSM4576pdfhgts
S_fonticola_GS2pdfhgts
S_liquefaciens_ATCC27592pdfhgts
S_liquefaciens_FDAARGOS125pdfhgts
S_liquefaciens_HUMV21pdfhgts
S_marcences_B3R3pdfhgts
S_marcences_CAV1492pdfhgts
S_marcences_DB11pdfhgts
S_marcences_FGI94pdfhgts
S_marcences_RSC14pdfhgts
S_marcences_SM39pdfhgts
S_marcences_SmUNAM836pdfhgts
S_marcences_WW4pdfhgts
S_multitudinisentens_RB25pdfhgts
S_nematodiphila_DZ0503SBS1pdfhgts
S_odorifera_DSM4582pdfhgts
S_plymuthica_3Re418pdfhgts
S_plymuthica_3RP8pdfhgts
S_plymuthica_4Rx13pdfhgts
S_plymuthica_AS9pdfhgts
S_plymuthica_PRI2cpdfhgts
S_plymuthica_S13pdfhgts
S_proteamaculans_568pdfhgts
S_rubidaea_1122pdfhgts
S_sp_AS12pdfhgts
S_sp_AS13pdfhgts
S_sp_FS14pdfhgts
S_sp_SCBIpdfhgts
S_sp_YD25pdfhgts
S_symbiotica_cinaracedripdfhgts
S_symbiotica_STspdfhgts
S_ureilytica_Lr54pdfhgts
Ecoli_K12pdfhgts
Yersinia_enterocolitica_8081pdfhgts

References


Funding

CAPES

CNPq Fundect