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Subgrouping Automata: Automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm

Paper ID Volume ID Publish Year Pages File Format Full-Text
15143 1381 2014 7 PDF Available
Title
Subgrouping Automata: Automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm
Abstract

•An algorithm is developed for automatic sequence subgrouping for given sequence set.•The algorithm basically utilizes phylogenetic tree from multiple sequence alignment.•The algorithm calculates all of pairwise sequence identities and statistical analysis.•The algorithm automatically determines optimum subgrouping node in phylogenetic tree.•The algorithm showed good performance for family- or superfamily-level sequence set.

Sequence subgrouping for a given sequence set can enable various informative tasks such as the functional discrimination of sequence subsets and the functional inference of unknown sequences. Because an identity threshold for sequence subgrouping may vary according to the given sequence set, it is highly desirable to construct a robust subgrouping algorithm which automatically identifies an optimal identity threshold and generates subgroups for a given sequence set. To meet this end, an automatic sequence subgrouping method, named ‘Subgrouping Automata’ was constructed. Firstly, tree analysis module analyzes the structure of tree and calculates the all possible subgroups in each node. Sequence similarity analysis module calculates average sequence similarity for all subgroups in each node. Representative sequence generation module finds a representative sequence using profile analysis and self-scoring for each subgroup. For all nodes, average sequence similarities are calculated and ‘Subgrouping Automata’ searches a node showing statistically maximum sequence similarity increase using Student's t-value. A node showing the maximum t-value, which gives the most significant differences in average sequence similarity between two adjacent nodes, is determined as an optimum subgrouping node in the phylogenetic tree. Further analysis showed that the optimum subgrouping node from SA prevents under-subgrouping and over-subgrouping.

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Keywords
Subgrouping; Protein family discrimination; Optimum subgrouping node; Phylogenetic tree; Statistical analysis
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Subgrouping Automata: Automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 48, February 2014, Pages 64–70
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us