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» Alignment of Non-Overlapping Sequences
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COLING
2008
15 years 4 months ago
A Local Alignment Kernel in the Context of NLP
This paper discusses local alignment kernels in the context of the relation extraction task. We define a local alignment kernel based on the Smith-Waterman measure as a sequence s...
Sophia Katrenko, Pieter W. Adriaans
CIBCB
2005
IEEE
15 years 8 months ago
The Homology Kernel: A Biologically Motivated Sequence Embedding into Euclidean Space
— Part of the challenge of modeling protein sequences is their discrete nature. Many of the most powerful statistical and learning techniques are applicable to points in a Euclid...
Eleazar Eskin, Sagi Snir
NAR
1998
76views more  NAR 1998»
15 years 2 months ago
U-insertion/deletion Edited Sequence Database
Uridine insertion/deletion RNA editing is a posttranscriptional RNA modification occurring in the mitochondria of kinetoplastid protozoa. The U-insertion/ deletion Edited Sequence...
Larry Simpson, Shirley H. Wang, Otavio H. Thiemann...
BMCBI
2010
106views more  BMCBI 2010»
15 years 3 months ago
Multiple structure alignment and consensus identification for proteins
Background: An algorithm is presented to compute a multiple structure alignment for a set of proteins and to generate a consensus (pseudo) protein which captures common substructu...
Ivaylo Ilinkin, Jieping Ye, Ravi Janardan
BMCBI
2008
113views more  BMCBI 2008»
15 years 3 months ago
Investigating selection on viruses: a statistical alignment approach
Background: Two problems complicate the study of selection in viral genomes: Firstly, the presence of genes in overlapping reading frames implies that selection in one reading fra...
Saskia de Groot, Thomas Mailund, Gerton Lunter, Jo...