scholarly journals LLE Based Pivot Selection for Similarity Search of Biological Data

2012 ◽  
Author(s):  
Kewei Ma ◽  
Honglong Xu ◽  
Pang Yue ◽  
Fuli Lei ◽  
Sheng Liu ◽  
...  
Keyword(s):  
Similarity Search ◽  
Biological Data ◽  
Pivot Selection ◽  
Selection For

scholarly journals Margin-Based Pivot Selection for Similarity Search Indexes

2010 ◽  
Vol E93-D (6) ◽  
pp. 1422-1432 ◽  
Author(s):  
Hisashi KURASAWA ◽  
Daiji FUKAGAWA ◽  
Atsuhiro TAKASU ◽  
Jun ADACHI
Keyword(s):  
Similarity Search ◽  
Pivot Selection ◽  
Selection For

scholarly journals RAFTS3: Rapid Alignment-Free Tool for Sequence Similarity Search

2016 ◽  
Author(s):  
Ricardo Assunção Vialle ◽  
Fábio de Oliveira Pedrosa ◽  
Vinicius Almir Weiss ◽  
Dieval Guizelini ◽  
Juliana Helena Tibaes ◽  
...  
Keyword(s):  
Similarity Search ◽  
Sequence Similarity ◽  
Biological Data ◽  
Amino Acid Residues ◽  
Binary Matrix ◽  
Protein Databases ◽  
Alignment Free ◽  
Large Databases ◽  
Search Tool ◽  
Time Required

AbstractBackgroundSimilarity search of a given protein sequence against a database is an essential task in genome analysis. Sequence alignment is the most used method to perform such analysis. Although this approach is efficient, the time required to perform searches against large databases is always a challenge. Alignment-free techniques offer alternatives to comparing sequences without the need of alignment.ResultsHere We developed RAFTS3, a fast protein similarity search tool that utilizes a filter step for candidate selection based on shared k-mers and a comparison measure using a binary matrix of co-occurrence of amino acid residues. RAFTS3performed searches many times faster than those with BLASTp against large protein databases, such as NR, Pfam or UniRef, with a small loss of sensitivity depending on the similarity degree of the sequences.ConclusionsRAFTS3 is a new alternative for fast comparison of proteinsequences genome annotation and biological data mining. The source code and the standalone files for Windows and Linux platform are available at: https://sourceforge.net/projects/rafts3/

Pivot Selection for Narrow Sketches by Optimization Algorithms

2020 ◽  
pp. 33-46
Author(s):  
Naoya Higuchi ◽  
Yasunobu Imamura ◽  
Vladimir Mic ◽  
Takeshi Shinohara ◽  
Kouichi Hirata ◽  
...  
Keyword(s):  
Optimization Algorithms ◽  
Pivot Selection ◽  
Selection For

Pivot selection for metric-space indexing

2016 ◽  
Vol 7 (2) ◽  
pp. 311-323 ◽  
Author(s):  
Rui Mao ◽  
Peihan Zhang ◽  
Xingliang Li ◽  
Xi Liu ◽  
Minhua Lu
Keyword(s):  
Metric Space ◽  
Pivot Selection ◽  
Selection For
Sign in / Sign up

Export Citation Format

Share Document