Software - Protein Homology Detection Through Alignment of Markov Random Fields - page 36

Fig. 3.4 An example alignment in the ranking file and the alignment detail file

' | ' Alignment score above 13.

' + ' Alignment score between 10 and 12.

' * ' Alignment score between 6 and 9.

' * ' Alignment score between 2 and 5.

' . ' Alignment score between 1 and 1.

−

' − ' Alignment score between 4 and 2.

− −

' = ' Alignment score below 5.

−

References

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J. Mol. Biol. 292(2), 195 - 202 (1999)
2. Wang, Z., et al.: Protein 8-class secondary structure prediction using conditional neural fields.
Proteomics 11(19), 3786

3792 (2011)
3. Jones, D.T., Ward, J.J.: Prediction of disordered regions in proteins from position specific score
matrices. Proteins Struct. Funct. Bioinf. 53(S6), 573

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578 (2003)

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