scholarly journals Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization

2018 ◽  
Vol 86 (4) ◽  
pp. 454-466 ◽  
Author(s):  
Maxwell W. Libbrecht ◽  
Jeffrey A. Bilmes ◽  
William Stafford Noble
Keyword(s):  
Protein Sequence ◽  
Sequence Data ◽  
Data Sets ◽  
Submodular Optimization ◽  
Protein Sequence Data

Universal trees based on large combined protein sequence data sets

10.1038/90129 ◽  
2001 ◽  
Vol 28 (3) ◽  
pp. 281-285 ◽  
Author(s):  
James R. Brown ◽  
Christophe J. Douady ◽  
Michael J. Italia ◽  
William E. Marshall ◽  
Michael J. Stanhope
Keyword(s):  
Protein Sequence ◽  
Sequence Data ◽  
Data Sets ◽  
Protein Sequence Data

scholarly journals Partitioning clustering algorithms for protein sequence data sets

2009 ◽  
Vol 2 (1) ◽  
Author(s):  
Sondes Fayech ◽  
Nadia Essoussi ◽  
Mohamed Limam
Keyword(s):  
Protein Sequence ◽  
Sequence Data ◽  
Clustering Algorithms ◽  
Data Sets ◽  
Protein Sequence Data

scholarly journals AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models

Entropy ◽  
2021 ◽  
Vol 23 (5) ◽  
pp. 530
Author(s):  
Milton Silva ◽  
Diogo Pratas ◽  
Armando J. Pinho
Keyword(s):  
Protein Sequence ◽  
Sequence Data ◽  
Specific Protein ◽  
General Purpose ◽  
Amino Acid Sequences ◽  
Input Size ◽  
Protein Sequence Data ◽  
Analysis Application ◽  
Straightforward Solution ◽  
Human Coronaviruses

Recently, the scientific community has witnessed a substantial increase in the generation of protein sequence data, triggering emergent challenges of increasing importance, namely efficient storage and improved data analysis. For both applications, data compression is a straightforward solution. However, in the literature, the number of specific protein sequence compressors is relatively low. Moreover, these specialized compressors marginally improve the compression ratio over the best general-purpose compressors. In this paper, we present AC2, a new lossless data compressor for protein (or amino acid) sequences. AC2 uses a neural network to mix experts with a stacked generalization approach and individual cache-hash memory models to the highest-context orders. Compared to the previous compressor (AC), we show gains of 2–9% and 6–7% in reference-free and reference-based modes, respectively. These gains come at the cost of three times slower computations. AC2 also improves memory usage against AC, with requirements about seven times lower, without being affected by the sequences’ input size. As an analysis application, we use AC2 to measure the similarity between each SARS-CoV-2 protein sequence with each viral protein sequence from the whole UniProt database. The results consistently show higher similarity to the pangolin coronavirus, followed by the bat and human coronaviruses, contributing with critical results to a current controversial subject. AC2 is available for free download under GPLv3 license.

scholarly journals Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences

1980 ◽  
Vol 187 (1) ◽  
pp. 65-74 ◽  
Author(s):  
D Penny ◽  
M D Hendy ◽  
L R Foulds
Keyword(s):  
Amino Acid ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Protein Sequences ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Minimal Tree ◽  
Protein Sequence Data

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127–150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151–166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

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