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Examining Protein Structure and Similarities by Spectral Analysis Technique
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Krista Collins
Published/Copyright:
September 17, 2006
The spectral envelope, a frequency based technique for analyzing categorical time series, is applied to amino acid sequences to examine their periodicity. The periodic signatures of such sequences is related to the secondary structure of the folding patterns in the gene. For a pair of sequences, we define a spectral envelope covariance which emphasizes the common periodicities in the two sequences. This is used to give a similarity measure for the two sequences which can then be used in a neighbour joining algorithm to construct a phylogeny. We apply the spectral methods to myoglobin sequences from primates and cetaceans. The spectral envelope reflects the structure of this protein and the tree constructed using spectral methods shows strong agreement with published trees.The spectral envelope can be used to explore similarities between and within different protein families. Since we do not require aligned sequences, the spectral methods can be used to create phylogenies across different protein families. We apply the method to 11 protein families from PANDIT obtaining a tree where the families are separated and the relationship among the families is given.
Published Online: 2006-9-17
©2011 Walter de Gruyter GmbH & Co. KG, Berlin/Boston
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Keywords for this article
spectral envelope;
protein secondary structure;
phylogenies;
spectral envelope covariance
Articles in the same Issue
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- Low-Order Conditional Independence Graphs for Inferring Genetic Networks
- A Generalized Clustering Problem, with Application to DNA Microarrays
- A Bayes Regression Approach to Array-CGH Data
- Statistical Selection of Maintenance Genes for Normalization of Gene Expressions
- Predicting the Strongest Domain-Domain Contact in Interacting Protein Pairs
- Dimension Reduction for Classification with Gene Expression Microarray Data
- A New Type of Stochastic Dependence Revealed in Gene Expression Data
- A New Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity
- Quality Optimised Analysis of General Paired Microarray Experiments
- Issues of Processing and Multiple Testing of SELDI-TOF MS Proteomic Data
- Cross-Validated Bagged Prediction of Survival
- Treatment of Uninformative Families in Mean Allele Sharing Tests for Linkage
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- Numerical Solutions for Patterns Statistics on Markov Chains
- A Heuristic Bayesian Method for Segmenting DNA Sequence Alignments and Detecting Evidence for Recombination and Gene Conversion
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- Treating Expression Levels of Different Genes as a Sample in Microarray Data Analysis: Is it Worth a Risk?
- Reader's Reaction
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