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Vaccine Epitope Coverage Subgroups File Format

The coverage calculation tool can analyze the coverage of your vaccine proteins compared against subsets of the target viral protein set. The subsets to be covered can be specified by having the tool make groups by looking at the names of the sequences in the target set, or by specifying and naming groups in a separate file.

Below is an example of such a file, one which groups the sequences in the sample input data according to country. Groups are specified as lists of sequence names; the first item in each list will be taken as the group name for reporting. Lists must be separated by one or more empty lines, and each item in each list must be on a separate line.

Kenya
A1.KE.99a
A1.KE.99b
A1.KE.00a
A1C.KE.0a
A1D.KE.0a
A1G.KE.9a
A2D.KE.9a

Cameroon
A1.CM._.a
F2.CM.95a
G.CM._.9a

Tanzania
A1.TZ.97a

Uganda
A1.UG._.a
A1.UG._.b
A1.UG._.c
D.UG._.0a
D.UG._.0b
D.UG.98.a
D.UG.99.a
D.UG.99.b
D.UG.99.c

United States
B.US.90.a
B.US._.Ba
B.US._.Ha
B.US._.La
B.US._.Na
B.US._.Pa
B.US.89.a
B.US._.Sa
B.US.90.b
B.US._.pa

Argentina
B.AR.98.a
B.AR.00.a
BF.AR.99a
BF.AR.99b

Australia
B.AU._.La
B.AU._.Lb
B.AU._.Lc
B.AU._.Ld
B.AU.87.a

Spain
B.ES._.5a
G.ES.00.a

France
B.FR.89.a
B.FR.94.a
C.FR.95.a

United Kingdom
B.GB.93.a
B.GB.94.a
B.GB.94.b
B.GB.93.b

Italy
B.IT._.2a
B.IT._.Na

Japan
B.JP._.na
B.JP._.nb

Korea
B.KR.00.a
B.KR.00.b
B.KR.00.c
B.KR.01.a
B.KR.02.a
B.KR.02.b
B.KR.02.c
B.KR.91.a
B.KR.93.a
B.KR.93.b
B.KR.95.a
B.KR.96.a
B.KR.97.a

Botswana
C.BW.00.a
C.BW.00.b
C.BW.96.a
C.BW.98.a
C.BW.99.a

India
C.IN.98.a
C.IN._.Sa

South Africa
C.ZA.98.a
C.ZA.98.b
C.ZA._.Za
C.ZA._.Zb
C.ZA._.Zc
C.ZA._.Zd
C.ZA._.Ze
C.ZA._.Zf
C.ZA.99.a
C.ZA.00.a
C.ZA.03.a
C.ZA.00.b
C.ZA.03.b
C.ZA.03.c
C.03ZASKa
C.04ZASKa
C.04ZASKb

Chad
D.TD.99.a

Sweden
J.SE.94.a

Congo
U.CD.83.a
A1DK.CD.a
A2G.CD.9a

United Arab Emirates
01_AE.CFa

Antigua and Barbuda
02_AG.CMa
02_AG.CMb


Gabon
11_cpx.Ga

Thailand
01B.TH._a
01C.TH._a

    
last modified: Wed Mar 26 18:07 2008


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