UsingGusWiki

Editing Gus Wiki

• do it often
• don't be shy about fixing things written on the wiki that can be improved. This is needed!
• instead of putting documentation in emails on the gusdev list, put it on this site, and provide a link in the mail
• remember that when you write something on the wiki, it is now communal property, and anybody can improve it.
• the only thing you should be cautious about is adding a new page. Its just that you can't really rename them. So think a little before you add one. Make it one that will be good to last a bit.

Using GBParser to load your annotation:

List of Tables and views that should get data from GBPareser plugin:

NAsequenceImp NAfeatureImp NAsequence ExternalNAsequence NAentry Organelle Genefeature Transcript NAfeature NAcomment NAGene NAProtein NALocation Source NASequenceOrganelle DbRefNAfeature NAfeatureNAGene NAfeatureComment NAPrimaryTranscript Miscellaneous NafeatureNAProtein ProteinFeature Repeats SeqVariation DBRefNASequence RNAType Immunoglobulin RNAStructure ExonFeature KeyWord SecondaryAccs NASequenceRef NASequenceKeyWord NAfeatureNAPT DNARegulatory DNAStructure STS

The main data storage takes place in 2 important tables:

NASequenceImp and NAfeatureIMP. As the name suggests, the NASequenceImp host data in sequence related area and the NAfeatureImp hosts data in feature related area. The other tables are either the child tables or the views on these 2 tables. They get data from various fields of these 2 tables.

The important views that store information on exon-intron data is NALocation and the na_feature_id of this table inherits data from NAfeatureImp table. The NAfeature view is the place to look for gene specific information.

One thing needs to be remembered is for each genbank file one na_sequence_id is generated. So in case you are uploading one chromosome as one file then you will have one id for that whereas for each gene one na_feature_id is generated.

Genefeature table stores the gene related information on those genes whose transcript is available. Transcript view stores tha data on the gene_name and protein_id information.

Apart from these there are various other tables/views whose name is self explanatory about the data it stores.