add Maize apollo curated gene set to gramene browser

[weix-cshl]

The community apollo curation project manually curated 109 maize gene models and generated the improved model as a GFF file, which can be attach as a custom track in Gramene's genome browser. In the mean time, we want to served them as a permanent track. To do it, we need to load the models to maize otherfeatures database.

As a test, I loaded them to the database of last release and displayed them on the previous browser (Grm60). Here is the an example:

http://paulaner.cshl.edu/Zea_mays/Location/View?r=3:2681283-2772776;db=core

[weix-cshl]

We missed ensemblgenome freeze deadline for June release (e97,eg44), because we found some data issue and had to clean the gff3 file up. But this also gave us more time to make sure our data is correct and our displaying strategy works.

We haven't got the protein sequence to validate the loaded models yet.

1. ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/gff3/zea_mays/curated_apollo_annotations_maize_v4.gff3 The gff3 was validated at http://genometools.org/cgi-bin/gff3validator.cgi

2. working directory brie:/home/weix/data/genomes/Zea_mays_AGPv4/ApolloCurated>

tested on colden:zea_mays_otherfeatures_60_95_7 perl ./load_genes_withAEDmultiP_from_gff3.pl -e ./ZmGrm60.registry -s zea_mays -l curated_genes curated_apollo_annotations_maize_v4.gff3

add entry to analysis_description in the otherfeatures database.

cat analysis_description.apollo 
76      Manually curated AGPv4 gene models with Apollo Annotation Editor        curated_apollo_annotations      1       {'multi_name' => 'curated_apollo_annotations','colour_key' => '[biotype]','caption' => 'curated_apollo_annotations','name' => 'Manually curated AGPv4 gene models with Apollo','label_key' => '[text_label] [display_label]','default' => {'MultiTop' => 'gene_label','contigviewbottom' => 'transcript_label','MultiBottom' => 'collapsed_label','contigviewtop' => 'gene_label','cytoview' => 'gene_label','alignsliceviewbottom' => 'as_collapsed_label'},'key' => 'apollo_curation'}

[weix-cshl]

Validated 269 proteins, loaded the 123 genes (271 transcripts) into live site database: colden:zea_mays_otherfeatures_61_96_7.

Here is a example http://ensembl.gramene.org/Zea_mays/Location/View?r=3:2707671-2714923;db=core

[marcelakarey]

Looks great. Thank you, Sharon!