Sequence search site for GenBank subset

[Dr. A. Jamie Cuticchia]

I am posting this question for a colleague who does not have newsgroup
access.  I can forward any posts or replies to him directly.

He is wondering whether there is a public web server available to perform
homology searches for a custom subset (ie. something other than those
subesets provided on the NCBI server (i.e.,  nr, dbest, htgs, etc.).

Basically he has a list of about 5000 accession numbers from GenBank which
he wants to exclusively search some new sequences against.

Thanks!

A. Jamie Cuticchia
ajc at iname.com