Re: [Gusdev-gusdev] GBParser failing to insert features

[Angel P. <an...@pc...>]

Fidel,
I'll look into this problem. It may take me a bit of time to do so (like 
a day or two) and get back to you with a full answer.
Angel

Fidel Salas wrote:

>I used the GBParser plugin to upload some GenBank entry which contains
>thousands of features.  However, only 33 features are found in the
>database.
>
>The features found in the database are exemplified by the following
>two features from the GenBank file:
>     gene            complement(142270..143373)
>                     /gene="lys9"
>                     /locus_tag="APE0193m"
>                     /db_xref="GeneID:1445541"
>     CDS             complement(142270..143373)
>                     /gene="lys9"
>                     /locus_tag="APE0193m"
>                     /codon_start=1
>                     /transl_table=11
>                     /product="saccharopine dehydrogenase"
>                     /protein_id="NP_147035.1"
>                     /db_xref="GI:14602185"
>                     /db_xref="GeneID:1445541"
>                     /translation="MVKIAVLGLGRVGLRAAYNLASRGFDVLGLDASNDAVSRARSLG
>                     LEARLYDVEGRKAGEYLRGQRVVAAFIALPYPVASRAVAHLSSAGIPVVVASIKPLRI
>                     DPGVVRAPILTEVGVSPGLSNVILYSMAAETGGGVSARVYVGSFGAREDGLLSHASTW
>                     RVEEMLEQYVTPAKLIQDGSEAVADPLDPSLWMEYSDPEHGVLECFPSQGLAGFISRR
>                     GSLFKELMECSLRRRGHLKVVLTMRGLGLLDSTPLKVSGCIVRPFDMAVKLVETRYPP
>                     DVGDVAVFTVEARRGGRWETLARASLRHGGGWSASSKMVGGASSAFAEVFAAEGLSEE
>                     EPGIIYPEDLYELGLAEKLLSLLPSHGVSLEVG"
>
>
>The ones that did not make it in look like this:
>     gene            complement(213..938)
>                     /locus_tag="APE0001"
>                     /db_xref="GeneID:1445602"
>     CDS             complement(213..938)
>                     /locus_tag="APE0001"
>                     /codon_start=1
>                     /transl_table=11
>                     /product="hypothetical protein"
>                     /protein_id="NP_146894.1"
>                     /db_xref="GI:14600380"
>                     /db_xref="GeneID:1445602"
>                     /translation="MVDILSSLLLSLPFGVIGFLLVLSPGSIWTPVKESIGYVYVSRR
>                     VTVKASKLLGSLTLLASLISFVVGAAYGITIQASTLALLLALITVVTVEYSMRLAEIE
>                     SLNQPVLEGFEPVGSIKLKYLTIILLVYLISIVFSIEGSLKLYSIGAYGTLASHLSIE
>                     ILAGYTVFLSVKRPEAYVIPGLSRETIELLQFFMPTSLSLIAIGVYMILAGFHMWWII
>                     LLAGVTTLFVVTMLIMINKEGKY"
>     gene            complement(938..1276)
>                     /locus_tag="APE0002"
>                     /db_xref="GeneID:1445577"
>
>The one element that is present in the features that are uploaded but
>absent in those that do not is the gene qualifier.
>
>Looking at the schema it is not obvious to me why the gene qualifier
>needs to be present in a feature in order to be uploaded.  Am I
>missing something more obvious?
>
>Thanks
>
>Fidel
>
>
>  
>