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:

1) Count a number of "transposase" as a product of CDS for all CDS in annotation file of each genome. -- it depends on annotation

2) Use a tool named OASIS. -- it depends on annotation

3) Use a web-server named ISsaga. -- it can analyse only 10 replicons at once

4) 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!



Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Browse other questions tagged or ask your own question.