Department of
Computing Science
 University of Alberta
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File Format

  1. Sequence file
  2. Secondary structure file
  3. Spin system file
  4. Adjacency information file

1.

Sequence file

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The sequence file is in FASTA format. The first line begins with a '>' followed by a comment. All the other lines are the amino acid sequence.

An example:

> Sequence Name and description
GSMDCEVNNGSSLRDECITNLLVFGFLQSCSDNSFRRELD
ALGHELPVLAPQWEGYDELQTDGNRSSHSRLGRIEADSES
QEDIIRNIARHLAQVGDSMDRSIPPGLVNGLALQLRNTSR

2.

Secondary structure file

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The secondary structure file we used is the PSIPRED output. In this file, the first line begins with a '#' followed by the description. Each of the other lines represents the secondary structure of one amino acid in the target protein sequence with the format "index amino_acid secondary_structure coil_prob helix_prob sheet_prob".

An example:

# PSIPRED VFORMAT (PSIPRED V2.3 by David Jones)
1 G C 0.986 0.010 0.010
2 S C 0.709 0.145 0.096
3 M C 0.666 0.143 0.211
4 D C 0.641 0.183 0.195
5 C C 0.683 0.127 0.205
6 E C 0.687 0.104 0.244
7 V C 0.738 0.078 0.215
8 N C 0.751 0.100 0.155
9 N C 0.834 0.087 0.071

3.

Spin system file

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The spin system file begins with a '>' followed by the number of spin systems and the intra chemical shift types and inter chemical shift types in the file. The possible chemical shift types are CA CB H N C HA. The suffix ".INTRA" and ".INTER" are used to differentiate the intra chemical shifts from inter chemcal shifts. Each of the other lines represents one spin system with the index and chemical shifts. The order of chemical shifts must follow the same order of chemical shift types in the first line.

An example:

>69 CA_INTRA CB_INTRA H N CA_INTER CB_INTER
1 53.900 30.700 8.440 123.800 53.100 30.600
2 60.100 30.300 8.290 121.800 53.900 30.700
3 51.900 38.700 8.110 122.100 59.200 58.600
...
67 58.700 35.800 8.020 125.200 54.000 28.700
68 60.300 0.000 7.700 129.500 58.700 35.800
69 56.600 27.000 7.130 108.200 59.000 36.000

4.

Adjacency information file

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The adj file contains all possible connections between spin systems. Each line has two number indexing the starting spin system and ending spin system. The same index number in the adj file, inter chemical shift file and spin system file must refer to the same spin system.

An example:

1 2
2 3
2 173
3 4
3 174
4 5
4 175
5 6
...

Last modified: May 09 2006 11:31:35  © Guohui Lin