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From: <ju...@cs...> - 2005-03-27 23:41:37
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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...
voice: (773) 834-3985
fax: (773) 702-6648
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