My first inclination would be to run LFASTA and then process the results
(available from Expasy).
The problem is that the LANL code is still buggy and has a length constraint
as yet undetermined.
That is of course if you have the sequence of the exons and the 30KB in its
We are interested in this problem of 'mapping to' as well.
The other issue is 'labelling' the exons that are mapped.
The TIGR site offers a code: at www.tigr.org/software
explained as follows:
AAT A tool for analyzing and annotating genomic
sequences. Huang, X., Adams, M.D., Zhou, H. and
Kerlavage, A.R. (1997) Genomics 46, 37-45. The AAT
package includes two sets of programs, one set
(DPS/NAP) for comparing the query sequence with a
protein database, and the other (DDS/GAP2) for
the query with a cDNA database. Each set contains a
database search program and a rigorous alignment
The database search program quickly identifies regions
the query sequence that are similar to a database
Then the alignment program constructs an optimal
for each region and the database sequence. The
program also reports the co-ordinates of exons in the
sequence. A WWW server for AAT is available at Michigan
Hope this is of interest,.
Paula Burch wrote in message <7c67qa$bg7 at gazette.bcm.tmc.edu>...
>Given a 30 kb region of genomic DNA, and sequence start and stop info
>on dozens of different exons that are of specific interest within this
>sequence, what's the easiest way to draw a quick picture showing
>visually just where all of these exons are, with labels?
>>This is quite different from exon prediction. We already know where
>the sequences of interest are - we need a summary to which we can
>easily refer. Drawing a map either by hand or with the computational
>tools I know takes a huge amount of time, though. Is there an existing
>tool to make it quick and easy?
>Paula E. Burch, Ph.D. Molecular Biology Computation Resource
>Baylor College of Medicine, BCMM M220 voice: 713.798.6023
>One Baylor Plaza, Houston, Texas 77030 fax: 713.798.4279
>http://mbcr.bcm.tmc.edu/pburch.html email: pburch at bcm.tmc.edu