Re: [Gusdev-gusdev] Assemblies

[Steve F. <sfi...@pc...>]

take a look at VirtualSequence

steve

Josef Jurek wrote:

>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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