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» Mining Protein Sequences for Motifs
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SDM
2003
SIAM
156views Data Mining» more  SDM 2003»
14 years 11 months ago
Detection of Underrepresented Biological Sequences using Class-Conditional Distribution Models
A labeled sequence data set related to a certain biological property is often biased and, therefore, does not completely capture its diversity in nature. To reduce this sampling b...
Slobodan Vucetic, Dragoljub Pokrajac, Hongbo Xie, ...
BMCBI
2007
106views more  BMCBI 2007»
14 years 9 months ago
Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach
Background: Selenocysteine and pyrrolysine are the 21st and 22nd amino acids, which are genetically encoded by stop codons. Since a number of microbial genomes have been completel...
Masashi Fujita, Hisaaki Mihara, Susumu Goto, Nobuy...
BMCBI
2006
137views more  BMCBI 2006»
14 years 9 months ago
Sigma: multiple alignment of weakly-conserved non-coding DNA sequence
Background: Existing tools for multiple-sequence alignment focus on aligning protein sequence or protein-coding DNA sequence, and are often based on extensions to Needleman-Wunsch...
Rahul Siddharthan
SSDBM
2006
IEEE
163views Database» more  SSDBM 2006»
15 years 3 months ago
ACache: Using Caching to Improve the Performance of Multiple Sequence Alignments
Multiple sequence alignment represents a class of powerful bioinformatics tools with many uses in computational biology ranging from discovery of characteristic motifs and conserv...
Xun Tu, Kajal T. Claypool, Cindy X. Chen
BMCBI
2002
108views more  BMCBI 2002»
14 years 9 months ago
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
Background: Covariance models (CMs) are probabilistic models of RNA secondary structure, analogous to profile hidden Markov models of linear sequence. The dynamic programming algo...
Sean R. Eddy