The best way to count a number of insertion sequences in a set of bacterial genomes

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5.1 years ago

little_more ▴ 70

I have a set of 414 GenBank genomes and I need to count a number of insertion sequences (ISs, transposases) in each of them. Is there any traditional way to perform such an analysis?

I came up with three possible ways:

Count a number of "transposase" as a product of CDS for all CDS in annotation file of each genome. -- it depends on annotation
Use a tool named OASIS. -- it depends on annotation
Use a web-server named ISsaga. -- it can analyse only 10 replicons at once
Perform blast(n or p) against ISfinder database and count a number of hits with low e-value. -- it seems not reliable

Any help is appreciated!

genome • 703 views

ADD COMMENT • link updated 5.1 years ago by Ram 43k • written 5.1 years ago by little_more ▴ 70

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what is the difference with your previous question ? How to find a number of TE in a set of genomes?

ADD REPLY • link 5.1 years ago by Pierre Lindenbaum 161k

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4 possible methods are listed here, no?

ADD REPLY • link 5.1 years ago by little_more ▴ 70

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