PSIST: a scalable approach to indexing protein structures using suffix trees

DOI10.1016/J.JPDC.2007.07.008MaRDI QIDQ436643zbMATH OpenOpenAlexFDO

Authors Feng Gao, Mohammed J. Zaki

Publication date 26 July 2012

Published in Journal of Parallel and Distributed Computing (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jpdc.2007.07.008

zbMATH Keywords

bioinformaticsexternal suffix treesprotein structure indexing

Mathematics Subject Classification ID

Learning and adaptive systems in artificial intelligence (68T05) Protein sequences, DNA sequences (92D20) Searching and sorting (68P10)

Recommendations

• Geometric suffix tree: indexing protein 3-D structures
• Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures
• Database indexing for large DNA and protein sequence collections
• SVM-based detection of distant protein structural relationships using pairwise probabilistic suffix trees
• Fast structural alignment of biomolecules using a hash table, n-grams and string descriptors

Cites work

• scientific article; zbMATH DE number 1945167 (Why is no real title available?)
• A Space-Economical Suffix Tree Construction Algorithm
• Algorithms on Strings, Trees and Sequences
• Database indexing for large DNA and protein sequence collections
• Distributed suffix trees
• On the sorting-complexity of suffix tree construction
• On-line construction of suffix trees
• PSIST: a scalable approach to indexing protein structures using suffix trees

Cited in

(5)

• SVM-based detection of distant protein structural relationships using pairwise probabilistic suffix trees
• PSIST: a scalable approach to indexing protein structures using suffix trees
• Geometric suffix tree: indexing protein 3-D structures
• Fast structural alignment of biomolecules using a hash table, n-grams and string descriptors
• Geometric Suffix Tree: A New Index Structure for Protein 3-D Structures

Describes a project that uses

Uses Software

• BLAST
• PSI-BLAST
• MUMMER
• SSAP
• MultiProt

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