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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

Thursday, 24 December 2009

Which is the Phage receptor? Fourth part.

Fourth comparison:TM4 phage genome

The Fourth comparison is with TM4 phage genome:

1- this is the result of Local (Smith-Waterman) comparison between the whole TM4 sequence and Proteins of Mycobacterium ulcerans Agy99:


By BugView
:
4208 comparisons for user's query sequence and
Mycobacterium ulcerans Agy99
Finished in 4629 seconds.

Highest score = 1695 for cds_3629 (118619508)
Second score = 1217 for cds_2549 (118618448)
Third score = 1094 for cds_3641 (118619519)



2-I have compared ,one by one, the indicated M.ulcerans cds with the TM4 phage genome:


1°cds_3629


cds_3629 is (MUL_4367):

PE-PGRS family protein (Mycobacterium ulcerans Agy99)
Other Aliases: MUL_4367
Annotation: NC_008611.1 (4845511..4848744, complement)
GeneID: 4550406



By BugView:
89 comparisons for cds_3629 (118619508)
Finished in 1 seconds.

Highest score = 266 for cds_24 (18496911)
Second score = 150 for cds_22 (18496909)
Third score = 128 for cds_8 (18496895)



cds_24


TM4_gp25
similar to L5 gp32 [Mycobacterium phage TM4]
Other Aliases: TM4_gp25, TM4_25
Other Designations: hypothetical protein
Annotation: NC_003387.1 (21422..22426)
GeneID: 932261



Accession...... GeneID

NP_569761.1932261




I have compared , the indicated cds 24 with the M.ulcerans genome:

By BugView
:
4208 comparisons for cds_24 (18496911)
Finished in 48 seconds.

Highest score = 299 for cds_331 (118616247)
Second score = 279 for cds_3309 (118619191)
Third score = 277 for cds_620 (118616526)






2°cds_2549

By BugView:
89 comparisons for cds_2549 (118618448)
Finished in 1 seconds.

Highest score = 244 for cds_24 (18496911)
Second score = 171 for cds_22 (18496909)
Third score = 137 for cds_28 (18496915)







3°cds_3641



By BugView:
89 comparisons for cds_3641 (118619519)
Finished in 1 seconds.

Highest score = 252 for cds_24 (18496911)
Second score = 163 for cds_22 (18496909)
Third score = 140 for cds_8 (18496895)