drawing a map

winhide winhide at sanbi.ac.za
Thu Mar 11 11:05:42 EST 1999


Hi Paula;

My first inclination would be to run LFASTA and then process the results
thru MAP/LANL
(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
entirety.

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
comparing
                     the query with a 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 co-ordinates of exons in the
query
                     sequence. A WWW server for AAT is available at Michigan
                     Tech.

Hope this is of interest,.

Win


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






More information about the Bio-soft mailing list