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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

Sunday 29 November 2009

Mycobacteriophage Genome Restriction Analysis

D29




NC_001900.gbk, 49136 bp. (LINEAR)

Restriction analysis 29/11/2009

pDRAW32 revision 1.1.101

Rebase containing 280 enzymes.

16 enzymes match enzyme selection criteria.

********************************************************

AatII (G_ACGT'C) [ZraI]
Cuts 1 time.
Cuts at position 26529.
Fragment sizes 26529, 22607.

AfeI (AGC'GCT) [Eco47III,Aor51HI]
Cuts 1 time.
Cuts at position 19096.
Fragment sizes 19096, 30040.

AflII (C'TTAA_G) [BfrI,BspTI,Bst98I,BstAFI,MspCI,Vha464I]
Cuts 1 time.
Cuts at position 26904.
Fragment sizes 26904, 22232.

AseI (AT'TA_AT) [VspI,PshBI]
Cuts 1 time.
Cuts at position 229.
Fragment sizes 229, 48907.

EcoRI (G'AATT_C)
Cuts 1 time.
Cuts at position 35257.
Fragment sizes 35257, 13879.

HpaI (GTT'AAC) [KspAI]
Cuts 1 time.
Cuts at position 4252.
Fragment sizes 4252, 44884.

MfeI (C'AATT_G) [MunI]
Cuts 2 times.
Cuts at positions 4345, 33476.
Fragment sizes 4345, 29131, 15660.

SacII (CC_GC'GG) [Cfr42I,KspI,Sfr303I,SgrBI,SstII]
Cuts 2 times.
Cuts at positions 7970, 32235.
Fragment sizes 7970, 24265, 16901.

SgrDI (CG'TCGA_CG)
Cuts 1 time.
Cuts at position 47838.
Fragment sizes 47838, 1298.

SmaI (CCC'GGG) [Cfr9I,TspMI,XmaI,XmaCI]
Cuts 2 times.
Cuts at positions 23175, 36011.
Fragment sizes 23175, 12836, 13125.

SpeI (A'CTAG_T) [AhlI,BcuI]
Cuts 2 times.
Cuts at positions 38318, 48289.
Fragment sizes 38318, 9971, 847.

SrfI (GCCC'GGGC)
Cuts 1 time.
Cuts at position 23175.
Fragment sizes 23175, 25961.

StuI (AGG'CCT) [AatI,Eco147I,PceI,SseBI]
[dcm methylated]
Cuts 2 times.
Cuts at positions 23559, 45643.
Fragment sizes 23559, 22084, 3493.

XbaI (T'CTAG_A)
[dam methylated]
Cuts 1 time.
Cuts at position 47494.
Fragment sizes 47494, 1642.

XmaI (C'CCGG_G) [SmaI,Cfr9I,TspMI,XmaCI]
Cuts 2 times.
Cuts at positions 23173, 36009.
Fragment sizes 23173, 12836, 13127.

ZraI (GAC'GTC) [AatII]
Cuts 1 time.
Cuts at position 26527.
Fragment sizes 26527, 22609.
L5




NC_001335.gbk, 52297 bp. (LINEAR)
Restriction analysis 29/11/2009
pDRAW32 revision 1.1.101
Rebase containing 280 enzymes.
21 enzymes match enzyme selection criteria.

********************************************************

AatII (G_ACGT'C) [ZraI]
Cuts 2 times.
Cuts at positions 23726, 40679.
Fragment sizes 23726, 16953, 11618.

AfeI (AGC'GCT) [Eco47III,Aor51HI]
Cuts 1 time.
Cuts at position 6414.
Fragment sizes 6414, 45883.

AflII (C'TTAA_G) [BfrI,BspTI,Bst98I,BstAFI,MspCI,Vha464I]
Cuts 1 time.
Cuts at position 15905.
Fragment sizes 15905, 36392.

ApoI (r'AATT_y) [AcsI,XapI]
Cuts 2 times.
Cuts at positions 44065, 48703.
Fragment sizes 44065, 4638, 3594.

BbeI (G_GCGC'C) [NarI,DinI,EgeI,EheI,KasI,Mly113I,SfoI]
Cuts 1 time.
Cuts at position 14171.
Fragment sizes 14171, 38126.

Bsu36I (CC'TnA_GG) [AxyI,Bse21I,Eco81I]
Cuts 2 times.
Cuts at positions 12530, 24833.
Fragment sizes 12530, 12303, 27464.

HpaI (GTT'AAC) [KspAI]
Cuts 1 time.
Cuts at position 49185.
Fragment sizes 49185, 3112.

KasI (G'GCGC_C) [NarI,BbeI,DinI,EgeI,EheI,Mly113I,SfoI]
Cuts 1 time.
Cuts at position 14167.
Fragment sizes 14167, 38130.

MreI (CG'CCGG_CG)
Cuts 1 time.
Cuts at position 16616.
Fragment sizes 16616, 35681.

NarI (GG'CG_CC) [BbeI,DinI,EgeI,EheI,KasI,Mly113I,SfoI]
Cuts 1 time.
Cuts at position 14168.
Fragment sizes 14168, 38129.

PasI (CC'CwG_GG)
Cuts 2 times.
Cuts at positions 26309, 43433.
Fragment sizes 26309, 17124, 8864.

PmlI (CAC'GTG) [PmaCI,AcvI,BbrPI,Eco72I,PspCI]
Cuts 2 times.
Cuts at positions 37771, 41672.
Fragment sizes 37771, 3901, 10625.

PvuI (CG_AT'CG) [BpvUI,MvrI,Ple19I]
Cuts 1 time.
Cuts at position 959.
Fragment sizes 959, 51338.

PvuII (CAG'CTG)
Cuts 2 times.
Cuts at positions 24091, 42988.
Fragment sizes 24091, 18897, 9309.

RsrII (CG'GwC_CG) [CpoI,CspI,Rsr2I]
Cuts 1 time.
Cuts at position 16814.
Fragment sizes 16814, 35483.

SacII (CC_GC'GG) [Cfr42I,KspI,Sfr303I,SgrBI,SstII]
Cuts 2 times.
Cuts at positions 31711, 52194.
Fragment sizes 31711, 20483, 103.

SfiI (GGCCn_nnn'nGGCC)
[dcm methylated]
Cuts 2 times.
Cuts at positions 11292, 39562.
Fragment sizes 11292, 28270, 12735.

SfoI (GGC'GCC) [NarI,BbeI,DinI,EgeI,EheI,KasI,Mly113I]
Cuts 1 time.
Cuts at position 14169.
Fragment sizes 14169, 38128.

SpeI (A'CTAG_T) [AhlI,BcuI]
Cuts 2 times.
Cuts at positions 5596, 37850.
Fragment sizes 5596, 32254, 14447.

XbaI (T'CTAG_A)
[dam methylated]
Cuts 2 times.
Cuts at positions 3150, 36267.
Fragment sizes 3150, 33117, 16030.

ZraI (GAC'GTC) [AatII]
Cuts 2 times.
Cuts at positions 23724, 40677.
Fragment sizes 23724, 16953, 11620.

Bxz2






TM4
Posted by Rodolfo Berretti at 19:52
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