Sequence-based predictions HEXA

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Revision as of 15:28, 27 May 2011 by Link (talk | contribs) (Prediction of disordered regions)

General Information

Secondary Structure Prediction

Prediction of disordered regions

Prediction of transmembrane alpha-helices and signal peptides

Prediction of GO terms

Secondary Structure prediction

Prediction of disordered regions

  • Disopred

Disopred predicts two disordered regions in our protein. The first region is at the beginning of the protein (first two residues) and the second region is at the end (last three regions). This prediction is probably wrong, because it is normal, that the electrons from the first and the last amino acids lack in the electron density map. So, our protein Hexosamidase A has no disordered regions.

Result of the Disopred prediction. * shows that this amino acid belongs to a disordered regions, whereas . signs for a non-disordered region.


  • POODLE

We decided to test several POODLE variants and to compare the results.

POODLE-I

POODLE-I predicted five disordered regions:

start position end position length
1 2 2
14 19 6
83 89 7
105 109 5
527 529 3


POODLE-L

POODLE-L found no disordered regions. Therefore, there is no disordered region with a length more than 40aa in our protein.


POODLE-S (High B-factor residues)

TODO

POODLE-S predicted five disordered regions:

start position end position length
0 2 2
13 19 7
83 88 6
105 109 5
526 529 4


POODLE-S (missing residues)

POODLE-S (missing residues) predicts regions as disordered, if there is a amino acid in the sequence record, but not on the electron density map.

Poodle-S found 6 disordered regions.

start position end position length
17 18 2
53 61 9
78 109 33
153 153 1
280 280 1
345 345 1


Graphical Output:

Prediction of POODLE-I
Prediction of POODLE-L
Prediction of POODLE-S (High B-factor residues)
Prediction of POODLE-S (missing residues)


TODO Comparison!!!

Prediction of transmembrane alpha-helices and signal peptides

Prediction of GO terms