Question: Best tool for bacterial genomic island prediction?
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gravatar for Kumar
19 months ago by
Kumar40
India
Kumar40 wrote:

Dear all, I have to predict genomic island sequence from 30 bacterial genomes. Further, I would like to compare those predicted DNA sequences among the same 30 bacterial genomes. Most of the genomic island prediction tools requires annotated file as input and gives result in tabular form. So, it is tedious to obtain DNA sequences from the tabular form.

Hence, could you please suggest me any genomic island prediction tool, which could give DNA sequence as Genomic island output.

ADD COMMENTlink modified 18 months ago by Biostar ♦♦ 20 • written 19 months ago by Kumar40

See this article, it compares some tools of prediction.

https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-9-329

The following one uses hmm-tool:

https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-7-142

Am I wrong and both of them require only annotated genomes?

In this case look at this post:

Find genomic Islands

ADD REPLYlink modified 19 months ago • written 19 months ago by natasha.sernova3.8k
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