Abstract:
The non-genealogical transfer of genetic information between prokaryotes is a frequent
and omnipresent event. The acquisition of foreign genomic segments may aid organisms
in adaptation to novel or extreme habitats with these rapid evolution events phenotypically
bene cial to the recipient. These regions of atypical and foreign origin are
vernacularly termed islands and are identi ed by their unique local genomic signature
or composition which di ers from the global host genomic signature. The SeqWord Genomic
Island Sni er program utilizes tetranucleotide frequency patterns and statistics to
identify regions of probable horizontal transfer. Optimum parameter values were determined
for this compositional-based island identi er to ensure acceptable levels of false
negative and false positive occurrence. Post-identi cation island analysis is demonstrated
with the aid of the LingvoCom package available from the SeqWord project. This island
identi er was furthermore compared with other existing transfer detection packages to
indicate relevance and reliability. The continued identi cation of islands in prokaryotic
genomes requires a novel and functional repository with the ability to expand as
newly sequenced archaeal/bacterial genomes are available. The amalgamation of a robust
database, convenient interface and island analysis tools presents a novel avenue in
prokaryotic island research. The Predicted Genomic Islands database currently houses
26,744 islands identi ed in 2,407 archaeal/bacterial genomes and is freely available from
http://pregi.bi.up.ac.za/. The database serves as an island information hub and collection
of analytical tools allowing users the ability to address a myriad of horizontal transfer
and island ontology research questions. Inclusion of various novel island information criteria
and analytical tools may distinguish this platform from extant island databases and
tools. Novel island comparison against the current content enables a rapid yet reliable
tool set in the age of brisk and economically e cient genome sequencing. The collection
of all island information in a single set allows for various avenues of research and
stratigraphy of islands by allowing for the deconstruction and inspection of layers in archaeal/
bacterial island communities and exchange between island hosts. The capability
of this island garage was previewed with novel island identi cation results and research
directions in an attempt to convey the future potential. This collection of island information
and tools may prove a reliable and innovative approach in variable elds of horizontal
transfer and island research with numerous applications and associations.
