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Abstract: Motivation Dynamic programming is the core algorithm of sequence comparison, alignment and linear hidden Markov model (HMM) training. For a pair of sequence lengths m and n, the problem can be solved readily in O(mn) time and O(mn) space. The checkpoint algorithm introduced by Grice, Hughey, and Speck (1997) runs in O(Lmn) time and O(Lm n) space, where L is a positive integer determined by m, n, and the amount of available workspace. The algorithm is appropriate for many string comparison... (Update)
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BibTeX entry: (Update)
@article{ wheeler00optimizing,
author = "Wheeler and Hughey",
title = "Optimizing Reduced-Space Sequence Analysis",
journal = "BIOINF: Bioinformatics",
volume = "16",
year = "2000",
url = "citeseer.ist.psu.edu/wheeler00optimizing.html" }
Citations (may not include all citations):270 The string-to-string correction problem (context) - Wagner, Fischer - 1974
171 Hidden Markov models in computational biology: Applications .. - Krogh, Brown et al. - 1994
148 the theory and computation of evolutionary distances (context) - Sellers - 1974
79 A linear space algorithm for computing maximal common subseq.. (context) - Hirschberg - 1975
78 An improved algorithm for matching biological sequences (context) - Gotoh - 1982
57 The SWISS-PROT protein sequence data bank and its supplement.. - Bairoch, Apweiler - 1998
46 Hidden Markov models for sequence analysis: Extension and an.. - Hughey, Krogh - 1996
36 Identi cation of common molecular subsequences (context) - Smith, Waterman - 1981
24 Optimal alignments in linear space (context) - Myers, Miller - 1988
7 Dynamic programming alignment accuracy - Holmes, Durbin - 1998
6 Parallel processing of biological sequence comparison algori.. (context) - Edmiston, Core et al. - 1988
6 Reduced space hidden markov model training - Tarnas, Hughey - 1998
5 Reduced space sequence alignment - Grice, Hughey et al. - 1997
1 On computing all suboptimal alignments (context) - Chao - 1998
1 A versatile divide and conquer technique for optimal string .. (context) - Powell, Allison et al. - 1999
1 Biological Seqeunce Analysis: Probabilistic models of protei.. (context) - Durbin, Eddy et al. - 1998
Documents on the same site (http://www.cse.ucsc.edu/research/compbio/papers/sam_doc/node2.html):
Hidden Markov Models for Detecting Remote Protein Homologies - Karplus, Barrett, Hughey (1999) (Correct)
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