Subsequences and ends ... and BLASTN

Doug Smith dsmith at ucsd.edu
Thu Feb 10 02:49:33 EST 2000


As some of you may have noticed, I have recently had troubles displaying
Subsequences in the Sequence FMAP Graphic display.

I found one solution to this problem:

simply include the tag:

Genomic_canonical

in the Sequence objects, both Source and Subsequence objects.

This tag comes up under 'Properties'.  Declaring this both shows the
subsequence objects in the appropriate column AND provides text display
of the 'Visible' information.

The 'Brief_identification' tag need not be used.

I am testing this further, but ... so far, so good ...

PS I tried this after noting a reference in the ACEDB article
in the Baxevanis 'Bioinformatics' book to NALUSDA 'magic tag' documentation,
which, although out of date, suggests that Subsequence column info is displayed
via 'Properties' tags ...



I now have another problem perhaps someone has experienced:

in displaying BLASTN homology data, the objects are displayed appropriately.
BUT with each manipulation that requires redrawing of the display, the
homology objects move to the right ... and thereby walk across the screen
to disappear into the sunset, never to be seen again ...

The BLASTN Method I am using, patterned after the Celegans method, is as
follows:

-----
Method : "BLASTN"
Colour	 "LIGHTBLUE"
Score_by_width
Score_bounds	 100 1000
Cluster
Right_priority	 5.2
Show_text
Blastn
Blixem_N
-----

any suggestions?

Thanks
  -Doug


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