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Table 1 Co-distribution analysis result of the example outlined in Fig. 1

From: A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions

Query protein A1 from species A

    

global BLAST run with E value of 0.000001

  

gi A1 taxid A, BLAST homologs found in k = 4 species

  

a: sorting range

     

4

b: gi of target protein

    

6

c: taxid of target protein

    

(above values for k and n for calculation of p)

l: number of species in which BLAST homologs were found

m: number of species identical with query protein

  

p: probability for co-distribution

    

e: 1 if the target protein is a direct BLAST ortholog of the query protein

f: protein annotation as

     

a

b

c

l

m

p

e

f

1

A1

A

4

4

6.67E-02

1

function one protein

2

A6

A

3

3

2.00E-01

0

function six protein

3

A8

A

2

2

4.00E-01

0

function eight protein

2

A2

A

4

3

5.33E-01

1

function two protein

5

A4

A

4

3

5.33E-01

0

function four protein

6

A5

A

2

1

5.33E-01

0

function five protein

7

A9

A

2

1

5.33E-01

0

function nine protein

8

A3

A

3

2

6.00E-01

0

function three protein

9

A7

A

3

2

6.00E-01

0

function seven protein

10

A0

A

1

1

6.67E-01

0

function zero protein