gusdev-gusdev

[GUSDEV] InsertSequenceFeature Issue in GUS3.5

[Kumar, S. <San...@ng...>]

Hi Group,
   I am having little problem with InsertSequenceFeature in our
environment.
   It is loading all features from the genBank file except "intron"
feature. I tried to look into the code and found that it is all together
skipping the "intron" feature from genBank file. Is that the issue with
"BioPerl"?
Did any one face this issue earlier?

The version of bioperl in our environment is :1.5.0
And I am using very first version of GUS3.5. Do we have any subsequent
release like GUS3.5.X?=20
And the file I am trying to load is related to MICROSPORIDIA organism
(NC_003238.gbf).
------
The genBank2gus.xml has entry for the intron like this:
<feature name=3D"intron" table=3D"DoTS::IntronFeature" so=3D"intron">
    <qualifier name=3D"allele" lost=3D"true"/>
    <qualifier name=3D"citation"/>
    <qualifier name=3D"cons_splice"/>
    <qualifier name=3D"evidence"/>
    <qualifier name=3D"function"/>
    <qualifier name=3D"gene" specialcase=3D"gene"/>
    <qualifier name=3D"label"/>
    <qualifier name=3D"locus_tag" column=3D"source_id"/>
    <qualifier name=3D"map"/>
    <qualifier name=3D"note" specialcase=3D"note"/>
    <qualifier name=3D"number" column=3D"num"/>
    <qualifier name=3D"old_locus_tag" lost=3D"true"/>
    <qualifier name=3D"standard_name"/>
    <qualifier name=3D"usedin"/>
    <qualifier name=3D"db_xref" specialcase=3D"dbxref"/>
  </feature>

And the intron entry in genBank file looks like this:
gene            complement(52254..52444)
                     /db_xref=3D"GeneID:860376"
                     /locus_tag=3D"ECU09_0395"
     CDS
join(complement(52254..52409),complement(52442..52444))
                     /db_xref=3D"GI:19173160"
                     /db_xref=3D"GeneID:860376"
                     /locus_tag=3D"ECU09_0395"
                     /codon_start=3D1
                     /protein_id=3D"NP_596963.1"
=20
/translation=3D"MGSRKTALVKTRLMRALKRNREIPAWKRMMKEHKGEYNRARRHW
                     RSKKLKIY"
                     /product=3D"60S RIBOSOMAL PROTEIN L39"
     misc_feature
join(complement(52260..52409),complement(52442..52444))
                     /db_xref=3D"CDD:11875"
                     /locus_tag=3D"ECU09_0395"
                     /note=3D"RPL39; Region: Ribosomal protein L39E
                     [Translation, ribosomal structure and biogenesis]"
     intron          complement(52410..52441)
                     /locus_tag=3D"ECU09_0395"
                     /note=3D"intron L39"

Any help will be appreciated.

Thanks
Sanjeev Kumar
Northrop Grumman

Re: [GUSDEV] InsertSequenceFeature Issue in GUS3.5

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

sanjeev-

take a look at the bioperl unflattener.  read the docs there.   we may 
have it configured to ignore introns, as they are implied by exons.  if 
you figure out how to re-configure the unflattener, and, think that ISF 
should support alternative unflattener configurations, we may need to 
add a command line option to ISF specifying how to configure the unflattener

steve

Kumar, Sanjeev wrote:

> Hi Group,
>    I am having little problem with InsertSequenceFeature in our 
> environment.
>    It is loading all features from the genBank file except "intron" 
> feature. I tried to look into the code and found that it is all 
> together skipping the "intron" feature from genBank file. Is that the 
> issue with "BioPerl"?
>
> Did any one face this issue earlier?
>
> The version of bioperl in our environment is :1.5.0
> And I am using very first version of GUS3.5. Do we have any subsequent 
> release like GUS3.5.X?
> And the file I am trying to load is related to MICROSPORIDIA organism 
> (NC_003238.gbf).
> ------
> *The genBank2gus.xml has entry for the intron like this*:
> <feature name="intron" table="DoTS::IntronFeature" so="intron">
>     <qualifier name="allele" lost="true"/>
>     <qualifier name="citation"/>
>     <qualifier name="cons_splice"/>
>     <qualifier name="evidence"/>
>     <qualifier name="function"/>
>     <qualifier name="gene" specialcase="gene"/>
>     <qualifier name="label"/>
>     <qualifier name="locus_tag" column="source_id"/>
>     <qualifier name="map"/>
>     <qualifier name="note" specialcase="note"/>
>     <qualifier name="number" column="num"/>
>     <qualifier name="old_locus_tag" lost="true"/>
>     <qualifier name="standard_name"/>
>     <qualifier name="usedin"/>
>     <qualifier name="db_xref" specialcase="dbxref"/>
>   </feature>
>
> *And the intron entry in genBank file looks like this:*
> gene            complement(52254..52444)
>                      /db_xref="GeneID:860376"
>                      /locus_tag="ECU09_0395"
>      CDS             
> join(complement(52254..52409),complement(52442..52444))
>                      /db_xref="GI:19173160"
>                      /db_xref="GeneID:860376"
>                      /locus_tag="ECU09_0395"
>                      /codon_start=1
>                      /protein_id="NP_596963.1"
>                      
> /translation="MGSRKTALVKTRLMRALKRNREIPAWKRMMKEHKGEYNRARRHW
>                      RSKKLKIY"
>                      /product="60S RIBOSOMAL PROTEIN L39"
>      misc_feature    
> join(complement(52260..52409),complement(52442..52444))
>                      /db_xref="CDD:11875"
>                      /locus_tag="ECU09_0395"
>                      /note="RPL39; Region: Ribosomal protein L39E
>                      [Translation, ribosomal structure and biogenesis]"
>      intron          complement(52410..52441)
>                      /locus_tag="ECU09_0395"
>                      /note="intron L39"
>
> Any help will be appreciated.
>
> Thanks
> Sanjeev Kumar
> Northrop Grumman
>