drawing a map

francis at CMMT.UBC.CA francis at CMMT.UBC.CA
Wed Mar 10 13:04:09 EST 1999


> 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?

Dear Paula,

to graphically represent your sequence data, I would recommend you give
Sequin a try (it's free,  so all you are risking is some of your time,
although I know this can be a rare ressource for many).  Sequin is a
DNA  submission tool, but you yan use it to view (and the idea is also
to _review_before_you_submit) your data.  Sequin is a network 'aware'
tool (although it does work 'stand-alone' on your PC/Mac or unix box),
and there is in it a very powerful style manager which allows you
configure colors, labels, width of ligns and so on.  You can download
GenBank records, and see what they look like, make your own style
sheet and, of course, put in your own data.

Sequin is available from our friends at the NCBI:

http:///www.ncbi.nlm.nih.gov/Sequin/

Where you will find help documentation, a quich startup guide, FAQ,
dowwnload info and the ability to add yourself to the sequin
notification e-mail list. There is also help available, at
info at ncbi.nlm.nih.gov

Because sequin is a sequence editinng tool, when you define new exons,
or new exon bounderies (which sequin doess not currently do) the
graphics is automatically updated -- it's actually a good idea to have a
graphics window up, as well as a text view of the GBFF (GenBank flat
file).

I know there are quite a few sequin users at Baylor, so maybe there is 
some local expertise you draw on ...

hope this helps,

francis


--
| B.F. Francis Ouellette                     tel: (604) 875-3815  | 
| Director, Bioinformatics Core Facility     fax: (604) 875-3800  | 
| Centre for Molecular Medicine and Therapeutics, UBC, Canada     |
| francis at cmmt.ubc.ca                     http://www.cmmt.ubc.ca  |




> 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
> 
> 




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