Matching Sequence with Inosines

Andrew T. Lloyd atlloyd at tcd.ie
Fri Jul 4 03:31:43 EST 1997

In article <33BA9791.3278 at charlie.cns.iit.edu>, Steven Gendel
<sgendel at charlie.cns.iit.edu> wrote:

> I have a published probe sequence that might be useful for my work.  The
> published sequence has several Inosine residues.  I would like to use
> something like FINDPATTERNS to compare this sequence to several genes in
> GenBank. What symbol should I use with GCG to account for the base
> "specificity" of the Inosines?  My inclination is to use N.  Is this a
> good idea?

I complements UCA.

The IUB/GCG code for ~G is H and according to Appendix III of
GCG 8.0 the complement of H is D.

Use D.

Andrew T. Lloyd  Irish National Centre for BioInformatics  INCBI
atlloyd at acer.gen.tcd.ie                   http://acer.gen.tcd.ie
Tel: (+353)-1-608-1969    EMBnet Ireland    Fax: (+353)-679-8558

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