[Gusdev-gusdev] Assemblies

[<ju...@cs...>]

I need to store some assembled contigs in GUS along
with the the sequences that these contigs were assembled from.
There are a few tables that appear that they are for
just such a purpose:

  DoTS::Assembly                 The Assembly view of NASequenceImp
                                 stores information and consensus sequences
                                 generated by assembling EST and mRNA sequences
                                 using the cap4 algorithm (Paracel)

  DoTS::AssemblyAnatomyPercent   Materialized view that maps Assemblies to
                                 the Anatomy ontology based on source library of
                                 the contained sequences

  DoTS::AssemblySNP              Table to record information about SNPs found
                                 in Assemblies

  DoTS::AssemblySequence         Table to hold the specific information about
                                 sequences contained in Assemblies

  DoTS::AssemblySequenceSNP      table that records the specifics of the
                                 putative SNP in this AssemblySequence

However, these tables seem to be intended for specific types of
assemblies using the Paracel cap4 software and/or assemblies
of EST/mRNA sequences.  I am using another assembler and assembling
genomic sequences.

As it looks as though these assembly tables were added for a specific
technique, I wonder if they could be expanded/generalized so that
one could store information for any type of assembly.

I suppose I could just use DoTS.Evidence to link my contigs
to the sequences that they were assembled from.

Has anyone any comments?

Thanks, Josef



Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

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