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BMCBI
2002
108views more  BMCBI 2002»
15 years 18 days 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
CVPR
2003
IEEE
16 years 2 months ago
Kernel Principal Angles for Classification Machines with Applications to Image Sequence Interpretation
We consider the problem of learning with instances defined over a space of sets of vectors. We derive a new positive definite kernel f(A B) defined over pairs of matrices A B base...
Lior Wolf, Amnon Shashua
102
Voted
BMCBI
2008
149views more  BMCBI 2008»
15 years 27 days ago
Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence
Background: Modern proteomes evolved by modification of pre-existing ones. It is extremely important to comparative biology that related proteins be identified as members of the s...
Adriano Barbosa-Silva, Venkata P. Satagopam, Reinh...
92
Voted
BMCBI
2010
134views more  BMCBI 2010»
15 years 27 days ago
Localizing triplet periodicity in DNA and cDNA sequences
Background: The protein-coding regions (coding exons) of a DNA sequence exhibit a triplet periodicity (TP) due to fact that coding exons contain a series of three nucleotide codon...
Liya Wang, Lincoln D. Stein
106
Voted
BMCBI
2010
86views more  BMCBI 2010»
15 years 27 days ago
The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand
Background: We study the usage of specific peptide platforms in protein composition. Using the pentapeptide as a unit of length, we find that in the universal proteome many pentap...
Giovanni Capone, Giuseppe Novello, Candida Fasano,...