How to view overlapping sequences

Keith Bradnam keith at thale.life.nottingham.ac.uk
Tue Nov 9 10:41:05 EST 1999



This is all new to me, so my apologies in advance if there is something
obvious that I have missed.

I have previously used xace and also AceBrowser to access ACeDB.  With the
complete C. elegans genome sequence you can use the Sequence Map class to
look at all the overlapping cosmid sequences.  Bringing up a sequence
display for any one cosmid sequence then allows you to move up or down to
adjacent cosmid sequences and therefore you can proceed along a
chromosome without having to launch separate windows for each overlapping 
sequence.

In contrast, when working with our Arabidopsis database, it seems that you
cannot move between overlapping sequences.  There is no Sequence Map class
for the Arabidopsis database and I was therefore curious as to how this
overlapping information for C. elegans is curated.

Are the relationships between overlapping sequences specified in the
models.wrm file?  More specifically in the Overlap_left and Overlap_right
tags of the Sequence class?

I know that in the GenBank entries of C. elegans cosmid sequences, there
are remarks that specify what the adjacent cosmids are, so I suppose in
building ACeDB, the necessary information could be extracted from this.

I would like to know how it would be possible to construct a similar
Sequence Map class for Arabidopsis so that it would be possible to
'scroll' through overlapping sequences.  This will become more important
by next year as the Arabidopsis genome project nears completion.

Hope someone can help me, thanks.

Keith B.


~  Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR)
~  University Park, University of Nottingham, NG7 2RD, UK
~  Tel: (0115) 951 3091 Web: http://synteny.nott.ac.uk/






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