Difference between revisions of "Task 3 (MSUD)"

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(→‎Result)
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=== Result ===
  
=== Result ===
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The results for ReProf and PsiPred predictions and the DSSP assignments are in the following folders:
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<code>
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/mnt/home/student/schillerl/MasterPractical/task3/reprof/
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/mnt/home/student/schillerl/MasterPractical/task3/psipred/
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/mnt/home/student/schillerl/MasterPractical/task3/dssp/
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</code>
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For P10775, ReProf was run with the protein sequence fasta file and the PSSMs (see <code>/mnt/home/student/schillerl/MasterPractical/task3/pssm/</code>) derived from big_80 and SwissProt as input. The following tables show the comparison of the prediction results to the secondary structure assignment of DSSP.
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{| class="wikitable" border="1" style="width:500px"
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|+ Comparison of ReProf prediction (fasta input) to DSSP assignment
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|-
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!secondary structure element !! recall !! precision !! f-measure
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|-
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|H || 0.719 || 0.585 || 0.645
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|-
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|E || 0.211 || 0.500 || 0.296
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|-
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|L || 0.616 || 0.654 || 0.635
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|}
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{| class="wikitable" border="1" style="width:500px"
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|+ Comparison of ReProf prediction (big_80 PSSM input) to DSSP assignment
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|-
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!secondary structure element !! recall !! precision !! f-measure
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|-
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|H || 0.944 || 0.889 || 0.916
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|-
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|E || 0.649 || 0.685 || 0.667
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|-
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|L || 0.826 || 0.866 || 0.846
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|}
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{| class="wikitable" border="1" style="width:500px"
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|+ Comparison of ReProf prediction (SwissProt PSSM input) to DSSP assignment
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|-
  +
!secondary structure element !! recall !! precision !! f-measure
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|-
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|H || 0.923 || 0.914 || 0.919
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|-
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|E || 0.807 || 0.523 || 0.634
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|-
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|L || 0.719 || 0.859 || 0.782
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|}
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The percentages of correctly identified secondary structure (H, E or L) for the three methods are 61 %, 86 % and 82 %. So for the remaining sequences, the method with the best performance (usage of PSSM derived from big_80 as input for ReProf) is used.
   
 
=== Discussion ===
  
=== Discussion ===

Revision as of 19:22, 15 May 2013

Secondary structure

Lab journal

Result

The results for ReProf and PsiPred predictions and the DSSP assignments are in the following folders:

/mnt/home/student/schillerl/MasterPractical/task3/reprof/

/mnt/home/student/schillerl/MasterPractical/task3/psipred/

/mnt/home/student/schillerl/MasterPractical/task3/dssp/


For P10775, ReProf was run with the protein sequence fasta file and the PSSMs (see /mnt/home/student/schillerl/MasterPractical/task3/pssm/) derived from big_80 and SwissProt as input. The following tables show the comparison of the prediction results to the secondary structure assignment of DSSP.


Comparison of ReProf prediction (fasta input) to DSSP assignment
secondary structure element recall precision f-measure
H 0.719 0.585 0.645
E 0.211 0.500 0.296
L 0.616 0.654 0.635


Comparison of ReProf prediction (big_80 PSSM input) to DSSP assignment
secondary structure element recall precision f-measure
H 0.944 0.889 0.916
E 0.649 0.685 0.667
L 0.826 0.866 0.846


Comparison of ReProf prediction (SwissProt PSSM input) to DSSP assignment
secondary structure element recall precision f-measure
H 0.923 0.914 0.919
E 0.807 0.523 0.634
L 0.719 0.859 0.782


The percentages of correctly identified secondary structure (H, E or L) for the three methods are 61 %, 86 % and 82 %. So for the remaining sequences, the method with the best performance (usage of PSSM derived from big_80 as input for ReProf) is used.

Discussion

Disordered protein

Lab journal

Result

Discussion

Transmembrane helices

Lab journal

Result

Discussion

Signal peptides

Lab journal

Result

Discussion

GO terms

Lab journal

Result

Discussion

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