Simulating early phase fragmented genome assembly

Question

[Anand Rao]

I am trying to see the effect of genome fragmentation on the number of gene calls that can be detected for a large gene family. For my research, I want to take the finished genome on which these genes have been predicted, and simply do the following: Break them into progressively smaller and more numerous fragments and count the number of intact genes I can still find.

For this, I seek your assistance with

1. Choosing the correct software to perform this fragmentation. I must point out here that I am not necessarily trying to break the genome into NGS type assemblies. If the tool allows the number of fragments to be user-defined, and uses whatever biological criteria in its black-box, that would suffice.
2. Post this fragmentation-simulation-step, I plan to simply perform something like a BLAT predicted protein Vs. fragmented genome with 100% match requirement to count the number of gene<=>protein correspondences that still exist despite the fragmentation.

Let me know if you think steps 1 and 2 are reasonable, and what (better) tools I may best use for them?

Answer 1

[sst]

1. I don't have any first-hand experience with this, but let me point you to this paper: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003998 -- the authors have done something similar in their benchmark steps to assess gene fragmentation with increasing sequence fragmentation. IIRC they sampled contig lengths from related species genomes to produce increasingly fragmented sequences.
2. Sure, you can do that. But keep in mind that if you have repeats there might not always be a 1:1 relationship.