We like to announce an email server for comparing a genomic DNA sequence
against SwissProt and dbEST using an analysis and annotation tool (AAT).
The tool includes two sets of programs, one for comparing the query
sequence with the protein database, and the other for comparing the query
with the cDNA database. Each set contains a fast database search program and
a rigorous alignment program. The database search program quickly identifies
regions of the query sequence that are similar to a database sequence.
Then the alignment program constructs an optimal alignment for each region
and the database sequence. The alignment program also reports the positions
of exons in the query sequence. Each alignment program handles the problem of
introns. The DNA-protein alignment program corrects frameshifts.
The AAT tool reduces the labor-intensive work of locating the exons
of the query sequence and improves the process of defining intron/exon
boundaries by using the wealth of available protein and cDNA data.
To receive instructions on using the AAT email server,
send a mail message to:
aat at cs.mtu.edu
Put the word 'HELP' on a single line in the body of the mail message.
The server is in a beta test stage. It is powered by a Sun Sparc 5.
A faster workstation will be available in a month or two.
Acknowledgments
The AAT tool was completed while X.H. was on sabbatical leave at TIGR.
Xiaoqiu Huang (Email: huang at cs.mtu.edu)
Dept. of Computer Science, Michigan Technological Univ., Houghton, MI 49931
