I have been looking for guidelines on reporting the results of an experiment that involves hundreds of thousands of BLAST searches, but I have not found anything.

My question is; how would you go about reporting and summarizing such a vast array of information? Say, you have 50000 separate sequences and you have ran a BLAST search on all of them, and for each you have received at least 2-3 significant results. How would you report the finding? Are there any packages and software that can be helpful in the process?

What is it that you want to learn from your results? Are you comfortable in any particular programming languages, such as R or python?

@Sean Davis: Yes. I am more than comfortable with programming in R. From my results, I want to learn whether each sequence gives me at least one hit with 100% identity.