Difference between revisions of "Sequence-based predictions HEXA"
(→Prediction of disordered regions) |
(→Prediction of disordered regions) |
||
| Line 27: | Line 27: | ||
=== Prediction of disordered regions === |
=== 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. |
||
| + | |||
| + | |||
| + | {{Bausteindesign|breite=10 |rand=1 |randfarbe=black |h-farbe=grey |t-farbe=black }} |
||
| + | |||
| + | |||
| + | conf: 970000000000000000000000000000000000000000000000000000000000 |
||
| + | pred: **.......................................................... |
||
| + | AA: MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSV |
||
| + | 10 20 30 40 50 60 |
||
| + | |||
| + | conf: 000000000000000003567778888887776530000000001122311000000000 |
||
| + | pred: ..................****************.......................... |
||
| + | AA: LDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTI |
||
| + | 70 80 90 100 110 120 |
||
| + | |||
| + | conf: 000000000000000000000000000000000000000000000000000000000000 |
||
| + | pred: ............................................................ |
||
| + | AA: NDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHY |
||
| + | 130 140 150 160 170 180 |
||
| + | |||
| + | conf: 000000000000000000000000000000000000000000000000000000000000 |
||
| + | pred: ............................................................ |
||
| + | AA: LPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVK |
||
| + | 190 200 210 220 230 240 |
||
=== Prediction of transmembrane alpha-helices and signal peptides === |
=== Prediction of transmembrane alpha-helices and signal peptides === |
||
Revision as of 16:48, 26 May 2011
Contents
General Information
Secondary Structure prediction
Prediction of disordered regions
- DISOPRED
Authors: Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT. Year: 2004 Source: [Prediction and functional analysis of native disorder in proteins from the three kingdoms of life.]
Description: This method is based on a neuronal network which was trained on high resolution X-ray structures from PDB. Disordered regions are regions, which appears in the sequence record, but their electrons are missing from electronic density map. This approach can also failed, because missing electrons can also arise because of the cristallization process. The method runs first a PsiBlast search against a filtered sequence database. Next, a profile for each residue is calculated and classified by using the trained neuronal network.
Prediction: As a prediction result you get a file with the predicted disordered region, the precision and recall. Furthermore you can a more detailed output. There you see the sequence, and the predictions and also numbers above the sequence (from 0 to 9 which shows you how likly your prediction is)
Input: If you run disopred on the console, you have to define the location of your database. The program needs as input your sequence in a file with fasta format.
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.
conf: 970000000000000000000000000000000000000000000000000000000000
pred: **..........................................................
AA: MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSV
10 20 30 40 50 60
conf: 000000000000000003567778888887776530000000001122311000000000 pred: ..................****************..........................
AA: LDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTI
70 80 90 100 110 120
conf: 000000000000000000000000000000000000000000000000000000000000 pred: ............................................................
AA: NDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHY
130 140 150 160 170 180
conf: 000000000000000000000000000000000000000000000000000000000000 pred: ............................................................
AA: LPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVK
190 200 210 220 230 240
