Difference between revisions of "Sequence-based predictions HEXA"

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(Prediction of disordered regions)
(Prediction of disordered regions)
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=== Prediction of disordered regions ===
 
=== Prediction of disordered regions ===
* Disopred
+
* 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.
 
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 }}
+
{{Bausteindesign|breite=80% |rand=2 |randfarbe=#CCCCCC |h-farbe=#FFFFFF |t-farbe=#000000 }}
   
 
conf: 970000000000000000000000000000000000000000000000000000000000
 
 
pred: **..........................................................
 
pred: **..........................................................
 
AA: MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSV
 
AA: MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSV
10 20 30 40 50 60
 
   
conf: 000000000000000003567778888887776530000000001122311000000000
 
 
pred: ..................****************..........................
 
pred: ..................****************..........................
 
AA: LDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTI
 
AA: LDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTI
70 80 90 100 110 120
 
   
conf: 000000000000000000000000000000000000000000000000000000000000
 
 
pred: ............................................................
 
pred: ............................................................
 
AA: NDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHY
 
AA: NDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHY
130 140 150 160 170 180
 
   
conf: 000000000000000000000000000000000000000000000000000000000000
 
 
pred: ............................................................
 
pred: ............................................................
 
AA: LPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVK
 
AA: LPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVK

Revision as of 16:51, 26 May 2011

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.


Template:Bausteindesign

pred: **..........................................................

 AA: MTSSRLWFSLLLAAAFAGRATALWPWPQNFQTSDQRYVLYPNNFQFQYDVSSAAQPGCSV

pred: ..................****************..........................

 AA: LDEAFQRYRDLLFGSGSWPRPYLTGKRHTLEKNVLVVSVVTPGCNQLPTLESVENYTLTI

pred: ............................................................

 AA: NDDQCLLLSETVWGALRGLETFSQLVWKSAEGTFFINKTEIEDFPRFPHRGLLLDTSRHY

pred: ............................................................

 AA: LPLSSILDTLDVMAYNKLNVFHWHLVDDPSFPYESFTFPELMRKGSYNPVTHIYTAQDVK
            190       200       210       220       230       240

Prediction of transmembrane alpha-helices and signal peptides

Prediction of GO terms