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» Contextual alignment of biological sequences
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AINA
2006
IEEE
15 years 12 months ago
Partitioned optimization algorithms for multiple sequence alignment
Multiple sequence alignment is an important and difficult problem in molecular biology and bioinformatics. In this paper, we propose a partitioning approach that significantly impr...
Yixin Chen, Yi Pan, Juan Chen, Wei Liu, Ling Chen
CIBCB
2005
IEEE
15 years 11 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
STOC
2000
ACM
156views Algorithms» more  STOC 2000»
15 years 10 months ago
Near optimal multiple alignment within a band in polynomial time
Multiple sequence alignment is a fundamental problem in computational biology. Because of its notorious difficulties, aligning sequences within a constant band (c-diagonal) is a ...
Ming Li, Bin Ma, Lusheng Wang
BMCBI
2006
137views more  BMCBI 2006»
15 years 5 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
BMCBI
2008
111views more  BMCBI 2008»
15 years 5 months ago
CBESW: Sequence Alignment on the Playstation 3
Background: The exponential growth of available biological data has caused bioinformatics to be rapidly moving towards a data-intensive, computational science. As a result, the co...
Adrianto Wirawan, Chee Keong Kwoh, Nim Tri Hieu, B...