Format 1 Description

This is the most common format used by existing prediction servers. Since your server likely produces more output than this bare format, you will need to parse the output to match this format.

Each protien prediction starts with a greater than symbol >followed by the number corresponding to the ID given in tmheval.fa ranging from 0 to 2246. If there are any helices predicted, the start and end residue numbers separated by a comma are given for each helix on a separate line. If there are no helices predicted for the protein, nothing is given and the next sequence can start.

>1
18,35
43,59
>2
>3
66,90
>4
22,39
43,62
69,88

Extra whitespace is generally not problematic:

OKAY:
>1
18, 35
43,59
>2

> 3

66,90
>4
22,39

43,62


69,88

But the record separator ">" must be at the beginning of a line

NOT OKAY:
 >1
18,35
43,59
 >2
 >3
66,90

NOT OKAY:
>1
18,35
43,59 >2
>3
66,90 >4
22,39
43,62
69,88