biolocal:2009 october science
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| Revision as of 15:19, 7 October 2009 (edit) Luca (Talk | contribs) (→06/10/2009) ← Previous diff |
Current revision (17:24, 16 October 2009) (edit) (undo) Luca (Talk | contribs) |
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| == [[07/10/2009]] == | == [[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. | * 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. | + | * Analysis of fragmented ORFs on PP1Y genome ('''Luca'''). ''Results suggest that some frame shift may be occurred during sequencing''. |
| + | |||
| + | == [[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'''). | ||
| + | |||
| + | == [[12/10/2009]] == | ||
| + | * Created a new website for share information of PP1Y genome to other people at http://www.ceinge.unina.it/~cozzuto/newVersion/index2.html ('''Luca'''). Created a list of genic pathways for each PP1Y replicon ('''Luca & Mauro'''). | ||
| + | |||
| + | == [[13/10/2009]] == | ||
| + | * Done genome browser of Nonomuraea plasmids at http://www.ceinge.unina.it/~cozzuto/newVersion/nonomuraea/index2.html ('''Luca'''). | ||
| + | * Made genome pictures with [[http://stothard.afns.ualberta.ca/cgview_server/ cgview]] , KEGG and COG annotations by GRC on Nonomuraea plasmids. | ||
| + | * Started InterProScan installation with relative data ('''Mauro'''). | ||
| + | |||
| + | == [[14/10/2009]] == | ||
| + | * Started new project called genomeannotator that includes all the scripts previously created to convert annotation results to a gff3 format ('''Luca'''). | ||
| + | |||
| + | == [[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'''). | ||
| + | |||
| + | == [[16/10/2009]] == | ||
| + | * Implemented in genomeannotator a new function: find neighborhood genomes. PP1Y sequences were analyzed by using this feature. ('''Luca''') | ||
Current revision
Contents[hide] |
[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
- Created a new website for share information of PP1Y genome to other people at http://www.ceinge.unina.it/~cozzuto/newVersion/index2.html (Luca). Created a list of genic pathways for each PP1Y replicon (Luca & Mauro).
[edit] 13/10/2009
- Done genome browser of Nonomuraea plasmids at http://www.ceinge.unina.it/~cozzuto/newVersion/nonomuraea/index2.html (Luca).
- Made genome pictures with [cgview] , KEGG and COG annotations by GRC on Nonomuraea plasmids.
- Started InterProScan installation with relative data (Mauro).
[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)
