How To Find Out Horizontally Transferred Genes In Bacteria?

Question

[Naren]

Dear all,
I have clustered all the proteins of 30 bacterial species from same genus using CD-HIT.
I have found out conserved (core), accessory, and unique set of clusters.
How can I determine whether the unique genes (exclusive to a particular bacteria species) are evolved or horizontally transferred from another species or strain?

Answer 1

[Michael]

This article seems to give a good review: http://www.annualreviews.org/doi/pdf/10.1146/annurev.micro.55.1.709

We can distinguish two general principles for detection:

• Based on sequence composition alone (e.g. atypical codon usage or base compositions)
• Based on sequence comparison (atypical homology with genes in other species, phylogenetic methods: e.g. comparison of phylogenetic trees of different gene sets)

In principle it seems that such methods work best on the DNA sequences of the genomes in question, if you don't have the sequences, you might have to sequence the genomes or at least some phylogenetic markers on DNA level.

[Naren]

Thanks, that review seems good but I have no access. try if you have.

[Michael]

try this: http://www.ncbi.nlm.nih.gov/books/NBK2228/

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