I just can answer your first question. From my experience it's only
timne consuming, but there exists no upper limit for a contig. I have
blasted already two complete microbial genomes to a database.
> I have got two questions:
>> 1. I would like to blast big contigs to a database.
> Is there a upper limit for the length of the query sequence? Or is it
> just time-consuming if I blast a big contig instead of overlapping parts
> of the contig?
>> 2. Has anyone here experience with the new "Blast" called Blat?
> Do you think it will be faster than BLAST?
> Are the results comparable?
>>> Thanks for your help!