Difference between revisions of "Task 4 (MSUD)"

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=== Results ===
  
=== Results ===
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The following table shows an overview of the structures used for building models, the scores of the structural alignment (RMSD and LGA_S - structure similarity score), and the scores of the sequence alignment (E-value, probability and sequence identity).
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{| class="wikitable" border="1" style="text-align:center;width:450px" align="center"
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!model !! RMSD !! LGA_S !! E-value !! probability !! sequence identity
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|-
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|1qs0 || 1.24 || 84.085 || 5.8E-94 || 100.0 || 38
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|-
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|1w85 || 1.77 || 78.356 || 8.3E-87 || 100.0 || 33
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|-
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|2ozl || 1.63 || 74.027 || 3.2E-69 || 100.0 || 27
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|-
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|2yic || 2.45 || 41.732 || 5.7E-47 || 100.0 || 16
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|-
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|3l84 || 2.01 || 32.412 || 6.5E-18 || 99.5 || 21
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|-
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|2q28 || 1.86 || 25.398 || 1.6E-08 || 97.9 || 13
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|-
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|1r9j || 1.73 || 30.095 || 1.1E-06 || 97.2 || 25
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|-
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|2vk8 || 2.12 || 21.990 || 3.7E-05 || 96.4 || 22
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|1t9b || 1.83 || 23.724 || 0.0011 || 94.9 || 18
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|2c31 || 2.00 || 21.849 || 0.011 || 92.7 || 21
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|}
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{| class="wikitable" border="1" style="text-align:center;width:450px" align="center"
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|+Correlations of structural to sequence alignement scores
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! !! e-value !! log10(e-value) !! probability !! sequence identity
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|-
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|'''RMSD''' || 0.15 || 0.49 || -0.19 || -0.74
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|-
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|'''LGA_S''' || -0.33 || -0.98 || 0.71 || 0.82
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|}
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As can be seen in the above table, the RMSD has a weak correlation to the logarithm of E-value and a higher correlation to sequence identity. The RMSD is lower, if the E-value is lower or the sequence identity is higher.
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The same tendency can be seen for the LGA_S score, but here the correlations are higher. The LGA_S score shows also a correlation to the probability in contrast to the RMSD.
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The signs are opposite for RMSD and LGA_S, because the RMSD is lower for higher similarity, but the LGA_S is higher.
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The relationship of LGA_S and E-value, the pair of scores with the highest correlation, for the 10 models is shown in the following plot.
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[[File:MSUD_cor_LGA-S_evalue.jpeg|400px|center]]
   
 
=== Discussion ===
  
=== Discussion ===

Revision as of 17:20, 30 May 2013

Explore structural alignments

Lab journal

Results

Discussion

Use structural alignments to evaluate sequence alignments

Lab journal

Results

The following table shows an overview of the structures used for building models, the scores of the structural alignment (RMSD and LGA_S - structure similarity score), and the scores of the sequence alignment (E-value, probability and sequence identity).


model RMSD LGA_S E-value probability sequence identity
1qs0 1.24 84.085 5.8E-94 100.0 38
1w85 1.77 78.356 8.3E-87 100.0 33
2ozl 1.63 74.027 3.2E-69 100.0 27
2yic 2.45 41.732 5.7E-47 100.0 16
3l84 2.01 32.412 6.5E-18 99.5 21
2q28 1.86 25.398 1.6E-08 97.9 13
1r9j 1.73 30.095 1.1E-06 97.2 25
2vk8 2.12 21.990 3.7E-05 96.4 22
1t9b 1.83 23.724 0.0011 94.9 18
2c31 2.00 21.849 0.011 92.7 21


Correlations of structural to sequence alignement scores
e-value log10(e-value) probability sequence identity
RMSD 0.15 0.49 -0.19 -0.74
LGA_S -0.33 -0.98 0.71 0.82


As can be seen in the above table, the RMSD has a weak correlation to the logarithm of E-value and a higher correlation to sequence identity. The RMSD is lower, if the E-value is lower or the sequence identity is higher.

The same tendency can be seen for the LGA_S score, but here the correlations are higher. The LGA_S score shows also a correlation to the probability in contrast to the RMSD.

The signs are opposite for RMSD and LGA_S, because the RMSD is lower for higher similarity, but the LGA_S is higher.


The relationship of LGA_S and E-value, the pair of scores with the highest correlation, for the 10 models is shown in the following plot.

MSUD cor LGA-S evalue.jpeg

Discussion

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