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!