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» Spatio-Temporal Alignment of Sequences
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BMCBI
2007
149views more  BMCBI 2007»
13 years 9 months ago
SAMPI: Protein Identification with Mass Spectra Alignments
Background: Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by tryps...
Hans-Michael Kaltenbach, Andreas Wilke, Sebastian ...
CPM
1994
Springer
123views Combinatorics» more  CPM 1994»
14 years 1 months ago
Computing all Suboptimal Alignments in Linear Space
Recently, a new compact representation for suboptimal alignments was proposed by Naor and Brutlag (1993). The kernel of that representation is a minimal directed acyclic graph (DAG...
Kun-Mao Chao
BIBM
2009
IEEE
118views Bioinformatics» more  BIBM 2009»
14 years 1 months ago
Inexact Local Alignment Search over Suffix Arrays
We describe an algorithm for finding approximate seeds for DNA homology searches. In contrast to previous algorithms that use exact or spaced seeds, our approximate seeds may conta...
Mohammadreza Ghodsi, Mihai Pop
BMCBI
2008
86views more  BMCBI 2008»
13 years 9 months ago
Subfamily specific conservation profiles for proteins based on n-gram patterns
Background: A new algorithm has been developed for generating conservation profiles that reflect the evolutionary history of the subfamily associated with a query sequence. It is ...
John K. Vries, Xiong Liu
ICPR
2006
IEEE
14 years 10 months ago
Affine Invariant Dynamic Time Warping and its Application to Online Rotated Handwriting Recognition
Dynamic Time Warping (DTW) has been widely used to align and compare two sequences. DTW can efficiently deal with local warp or deformation between sequences. However, it can'...
Yu Qiao, Makoto Yasuhara