BAC annotation strategy

Question

[abhijit.synl]

Hello All,

I have a strategy question related to BAC annotation. I have 500 BAC sequences from a single maize line to annotate. I am faced with a strategy dilemma.

1) Put all the BAC sequences in one file, create a multi-fasta file and run the annotation.

2) Go about the annotation on a per BAC basis, One BAC sequence per file.

I would like to know the pros and cons of both strategies if anyone has done such a thing. What i want to know is that when we run a set of evidences on a BAC multi-fasta file, is the mapping of a particular evidence to a particular BAC, dependent on the probability of its mapping to other BACs in the multi-fasta file.

Thank you all Abhijit