biolocal:2009 october science

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[edit] 06/10/2009

  • New Argo genome browser for PP1Y is installed (Luca). In this way all the functionality of Argo genome browser are available. The site is at http://www.ceinge.unina.it/~cozzuto/newVersion/PP1Y/
  • Annotation of protein genes on nomomuraea plasmids (Luca). GRC tool was used with Uniref50 database.

[edit] 07/10/2009

  • Annotation of COG genes on PP1Y genome (Luca). GRC tool was used with COG database to annotate PPY replicons. A php script in was created in /biodev/.project/tools/ folder named addCog2tbl.php to add COG annotation to the tbl file and to produce statistics on COG classes.
  • Analysis of fragmented ORFs on PP1Y genome (Luca). Results suggest that some frame shift may be occurred during sequencing.

[edit] 08/10/2009

  • Added COG annotations and initial contigs to the Argo browser on PP1Y genome (Luca).
  • Making GRC annotations with KEGG database on PP1Y genome (Luca).

[edit] 12/10/2009

[edit] 13/10/2009

[edit] 14/10/2009

  • Started new project called genomeannotator that includes all the scripts previously created to convert annotation results to a gff3 format (Luca).

[edit] 15/10/2009

  • Implemented in genomeannotator new functions: join different gene predictions, search duplicated and fragmented genes. PP1Y sequences were scanned for duplicated and fragmented genes. Added in Argo a new feature called MULTIPLE that is the union of all gene predictions (Luca).

[edit] 16/10/2009

  • Implemented in genomeannotator a new function: find neighborhood genomes. PP1Y sequences were analyzed by using this feature. (Luca)
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