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"In silico"


From Wikipedia
If the target host* of a phage therapy treatment is not an animal the term "biocontrol" (as in phage-mediated biocontrol of bacteria) is usually employed, rather than "phage therapy".

In silico
From:"Genomics,Proteomics and Clinical Bacteriology",N.Woodford and Alan P.Johnson

Phrase that emphasizes the fact that many molecular biologists spend increasing amounts of their time in front of a computer screen, generating hypotheses that can subsequently be tested and (hopefully) confirmed in the laboratory.


Phage Therapy is influenced by:

Phage therapy is influenced by:

Country : the epidemiological situation is different from country to country in terms of circulating bacteria and bacteriophages. Example: lytic phages from Italy may be no active on the same bacteria (genus and species) isolated from another country and vice versa.
Temporariness
Mutation rate
Phenotypical delay
Phage cocktail

My point of view

Monday, 10 August 2009

How to explore a Phage "In Silico": Mycobacterium phage D29 . Step 1




All steps are the same for all phages.




*Mycobacterium phage D29


(dsDNA viruses, no RNA stage; Caudovirales; Siphoviridae; L5-like viruses)



*
Go to
DBGET Search
write : Mycobacterium phage D29
open and the Page is showing:

*In DNA sequence open NCBI and the complete genome is ready with CDS and the relative sequences in amino acids.

*In KEGG Vgenome open
NC_001900
and the page is ready with :

  Number of nucleotides:         49136

Number of protein genes: 79

Number of RNA genes: 5

G+C content: 63.5%




*Go to ITVC index viruses for "L5 -like viruses"
and see the other members and Mycobacterium phage L5.


*Go to NCBI Map, select Virus. The Virus page is open , select in the window Siphoviridae, open and all phage genomes of this Family are showing.



*Go to EBI Genomes write : Mycobacterium phage D29 and open.
The page with concise data is showing.


*Go to HAMAP proteomes and write in the upper window : Mycobacterium phage D29 and open.
The page with genes and proteins is showing.



*Go to Genome online database
and in the Google window write: Mycobacterium phage D29 , select web data and open. All data on Mycobacteriophage D29 are showing.