FragHMMent - Info and Help

Output formats

Residue-residue prediction (CASP format) format

Contact predictions are supplied in the CASP format where each row contain 
one prediction in the following format:

i  j  d1  d2  p

where
    - i and j are two positions in the submitted target sequence predicted to be in contact
    - d1 and d2 indicate the range of Cb-Cb distances predicted (always 0 and 8)
    - p is the contact prediction score (between 0 and 1, high values indicating high confidence) 
	

Descriptor alignment format

Example:
1qo0d_#107    31-38;54-60;63-67/D84-D91;D103-D109;D112-D116;
1.0142722380464209

Descriptor group: 1qo0d_#107 is the name of the assigned local
descriptor group. It has the form "domain#center", where "domain" is
the name of an ASTRAL domain and "center" is the residue that the
local neighborhood is centered on.

Target positions: 31-38;54-60;63-67 are the sections of the target
where the fragments of the local descriptor group 1qo0d_#107 are
assigned. I.e. fragment 1 is assigned from position 31 to position 38,
fragment 2 from position 54 to 60 and fragment 3 from 63 to 67.

Positions for 3D coordinates: D84-D91;D103-D109;D112-D116; are
sections in the coordinate file of domain 1qo0d_ that coorespond to
fragments in the local descriptor 1qo0d_#107. This information should
be used to transfer structural information from the local descriptor
to the target according to alignment (e.g. coordinates for position
D84 should be transferred to position 31 on the target, D85 to 32,
D109 to 60, D112 to 63, etc.)

Alignment score: 1.0142722380464209 is the score obtained by the HMM
representing the local descriptor group 1qo0d_#107. 
	

Vector format

The Feature vector format is an alternative representation of the 
Descriptor alignment format described above.

Example:
TARGET T0387
0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0

The first line contains the target name, while the second line contains the 
feature vector. Each position in the vector represents a local descriptor group 
(same order as in this file list_of_purged_names.txt). Each integer represents 
the number of different position in which the corresponding local descriptor group 
obtained an alignment score above the assignment threshold.