Re: [Gusdev-gusdev] Location of gene prediction program

[Sucheta T. <su...@vb...>]

Steve,

Following is the data snippet.

*******************

                    /translation="MEAADAADSVLHGDLLECVLLRVPHGELTASPALVSREWRRAAR
                    EAHQRHRRRRRHLPCLVAHVHGAAAGVGRSTHVYDPRAGAWASDGWRVAGALPVRRCA
                    CAGGDRVYALSLASMAVSEDAVGAAWRELPPPRVWRVDPVVAAVGPHVVVLGGGCGAT
                    AAAGVVEVLDEGAGWATCPPMPAPLASRWVSSAASERRVYVVERRTGWASWFDPAARQ
                    WGPARQLQLPEGNNTASVESWAACGVTTSGGGGASERLLVLAGGGGGKVSLWGVDGDT
                    LLLDAEANNTSMPPEMSERLGGAGSIAAAAAGAASGYVYNASEPSKGAVRYELVDAEV
                    GGGHGSYSDSDSKNGRHEKTWGKRSSGGSRWEWEWLPCPPAAAAAMSTSSSAVVVFAC
                    CGSSSAPNK"
    gene            join(22480..22704,23721..23786)
                    /gene="OJ1342_D02.4"
    misc_feature    join(22480..22704,23721..23786)
                    /gene="OJ1342_D02.4"
                    /note="gag-pol polyprotein-like"
    gene            complement(25925..26257)
                    /gene="OJ1342_D02.5"
    mRNA            complement(<25925..>26257)
                    /gene="OJ1342_D02.5"
                    /note="start and end point are not identified"
    CDS             complement(25925..26257)
                    /gene="OJ1342_D02.5"
                    /note="predicted by FGENESH etc."
                    /codon_start=1
                    /product="hypothetical protein"
                    /protein_id="BAD19559.1"
                    /db_xref="GI:47497506"

*************************************

In this case the prediction was by FGENESH.

Sucheta


At 02:43 PM 7/1/2004 -0400, you wrote:
>sucheta-
>
>can you clarify where the prediction_program_algorithm is used in your 
>data.  Is it in a genbank file?  can you provide a snippet of that data?
>
>thanks,
>steve
>
>Sucheta Tripathy wrote:
>
>>Hi,
>>
>>My most immediate concern is about locating where the 
>>prediction_program_algorithm is stored in GUS. Here I mean the gene 
>>prediction programs like genscan, glimmer etc.
>>
>>In some of the views which gets data from NAFeatureIMP though I see 
>>prediction_algorithm_id but that refers to core.algorithm, and which just 
>>stores the plugin information, that are used in the current project.
>>For example in our core.algorithm table the following is the data:
>>id                                                         Name
>>===                                                     =====
>>1                                                        SQL*PLUS
>>2                                                        GA-Plugin
>>3 GUS::Common::Plugin::SubmitRow
>>4 GUS::Common::Plugin::LoadTaxon
>>5 GUS::GOPredict::Plugin::LoadGoOntology
>>....
>>So the prediction_algorithm_id is wrongly pointing to core.algorithm??
>>
>>
>>thanks
>>Sucheta
>>
>>
>>
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>