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We have sequenced the genome of 200 bacterial strains belonging to the same species, a swine bacterial pathogen. In a previous work, it was observed that a protein family of adhesins is present in some of these strains. Each strain has multiple copies separated in their genome. Genetic differences have been observed among the DNA sequence in the different strains. Since some mobile genetic elements are present near these genes, it is possible that they are playing a role in the molecular evolution of this protein family.

How could I add additional evidences that this is a putative genomic island?

Some references would be also appreciated.

Thanks

UPDATE: For each strain, I thought about extracting the genomic region were these genes are located, maybe 8 Kb up- and down-stream of the gene. Then, running a miriad of tools to try to predict some of these island-associated elements. However, assuming that these "sequence-based" tools need the entire genome sequence, is it possible that I run them using the whole genome sequence and then focus on certain selected genomic regions?

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  • $\begingroup$ Check this. You might find tools you are looking for. For second question, you can do cheap trick by just separate your area of interest from your whole genome and then feed that sequence as single genome into tool again. $\endgroup$
    – Dexter
    Commented Sep 21, 2015 at 15:37

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