-
1
-
-
0025183708
-
Basic local alignment search tool
-
S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman. Basic local alignment search tool. Journal of Molecular Biology, 215:403-410, 1990.
-
(1990)
Journal of Molecular Biology
, vol.215
, pp. 403-410
-
-
Altschul, S.1
Gish, W.2
Miller, W.3
Myers, E.4
Lipman, D.5
-
2
-
-
0030801002
-
Gapped blast and psi-blast: a new generation of protein database search programs
-
S. Altschul, T. Madden, R. Schffer, J.Zhang, Z.Zhang, W.Miller, and D. Lipman. Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res, 25:3389-3402, 1997.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.1
Madden, T.2
Schffer, R.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.7
-
3
-
-
57149141135
-
Approximate embedding-based subsequence matching of time series
-
V. Athitsos, P. Papapetrou, M. Potamias, G. Kollios, and D. Gunopulos. Approximate embedding-based subsequence matching of time series. In ACM International Conference on Management of Data (SIGMOD), pages 365-378, 2008.
-
(2008)
ACM International Conference on Management of Data (SIGMOD)
, pp. 365-378
-
-
Athitsos, V.1
Papapetrou, P.2
Potamias, M.3
Kollios, G.4
Gunopulos, D.5
-
4
-
-
0017547820
-
A fast string searching algorithm
-
R. S. Boyer and J. S. Moore. A fast string searching algorithm. Commun. ACM, 20(10):762-772, 1977.
-
(1977)
Commun. ACM
, vol.20
, Issue.10
, pp. 762-772
-
-
Boyer, R.S.1
Moore, J.S.2
-
5
-
-
0032644644
-
q-gram based database searching using a suffix array (quasar)
-
S. Burkhardt, A. Crauser, P. Ferragina, H.-P. Lenhof, E. Rivals, and M. Vingron. q-gram based database searching using a suffix array (quasar). In International Conference on Computational Molecular Biology (RECOMB), pages 77-83, 1999.
-
(1999)
International Conference on Computational Molecular Biology (RECOMB)
, pp. 77-83
-
-
Burkhardt, S.1
Crauser, A.2
Ferragina, P.3
Lenhof, H.-P.4
Rivals, E.5
Vingron, M.6
-
6
-
-
0141717105
-
Better filtering with gapped q-grams
-
S. Burkhardt and J. Kärkkaäinen. Better filtering with gapped q-grams. Fundam. Inf., 56(1,2):51-70, 2002.
-
(2002)
Fundam. Inf
, vol.56
, Issue.1-2
, pp. 51-70
-
-
Burkhardt, S.1
Kärkkaäinen, J.2
-
8
-
-
33751181225
-
DSIM: A distance-based indexing method for genomic sequences
-
X. Cao, B. C. Ooi, A. Tung, H. H. Pang, and K.-L. Tan. DSIM: A distance-based indexing method for genomic sequences. In IEEE Symposium on Bioinformatics and Bioengineering (BIBE), pages 97-104, 2005.
-
(2005)
IEEE Symposium on Bioinformatics and Bioengineering (BIBE)
, pp. 97-104
-
-
Cao, X.1
Ooi, B.C.2
Tung, A.3
Pang, H.H.4
Tan, K.-L.5
-
9
-
-
84865098967
-
Sublinear expected time approximate string matching and biological applications
-
Technical Report CSD-91-654, University of California at Berkeley
-
W. I. Chang and E. L. Lawler. Sublinear expected time approximate string matching and biological applications. Technical Report CSD-91-654, University of California at Berkeley, 1991.
-
(1991)
-
-
Chang, W.I.1
Lawler, E.L.2
-
11
-
-
0036306157
-
SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size
-
E. Giladi, M. G. Walker, J. Z. Wang, and W. Volkmuth. SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size. Bioinformatics, 18(6):873-877, 2002.
-
(2002)
Bioinformatics
, vol.18
, Issue.6
, pp. 873-877
-
-
Giladi, E.1
Walker, M.G.2
Wang, J.Z.3
Volkmuth, W.4
-
12
-
-
14644425852
-
The smallest uniform upper bound on the distance between the mean and the median of the binomial and poisson distributions
-
K. Hamza. The smallest uniform upper bound on the distance between the mean and the median of the binomial and poisson distributions. Statistics and Probability Letters, 23(1):21-25, 1995.
-
(1995)
Statistics and Probability Letters
, vol.23
, Issue.1
, pp. 21-25
-
-
Hamza, K.1
-
13
-
-
0037314081
-
A generalized global alignment algorithm
-
X. Huang and K.-M. Chao. A generalized global alignment algorithm. Bioinformatics, 19(2):228-233, 2003.
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 228-233
-
-
Huang, X.1
Chao, K.-M.2
-
14
-
-
0034139837
-
Jongeneel. Searching the expressed sequence tag (est) databases: Panning for genes
-
C. V. Jongeneel. Searching the expressed sequence tag (est) databases: Panning for genes. Bioinformatics, 1:76-92, 2000.
-
(2000)
Bioinformatics
, vol.1
, pp. 76-92
-
-
Jongeneel, C.V.1
-
15
-
-
1842667856
-
Pash: Efficient genome-scale sequence anchoring by positional hashing
-
K. J. Kalafus, A. R. Jackson, and A. Milosavljevic. Pash: Efficient genome-scale sequence anchoring by positional hashing. Genome Resources, 14(4):672678, 2004.
-
(2004)
Genome Resources
, vol.14
, Issue.4
, pp. 672678
-
-
Kalafus, K.J.1
Jackson, A.R.2
Milosavljevic, A.3
-
16
-
-
0022030599
-
Efficient randomized pattern-matching algorithms
-
R. M. Karp and M. O. Rabin. Efficient randomized pattern-matching algorithms. IBM J. Res. Dev., 31(2):249-260, 1987.
-
(1987)
IBM J. Res. Dev
, vol.31
, Issue.2
, pp. 249-260
-
-
Karp, R.M.1
Rabin, M.O.2
-
17
-
-
84865078574
-
Resource BLAT-The BLAST-Like Alignment Tool
-
W. J. Kent. Resource BLAT-The BLAST-Like Alignment Tool. Genome Research, 2002.
-
(2002)
Genome Research
-
-
Kent, W.J.1
-
18
-
-
33745621089
-
n-gram/2l: A space and time efficient two-level n-gram inverted index structure
-
M.-S. Kim, K.-Y. Whang, J.-G. Lee, and M.-J. Lee. n-gram/2l: A space and time efficient two-level n-gram inverted index structure. In International Conference on Very Large Data Bases (VLDB), pages 325-336, 2005.
-
(2005)
International Conference on Very Large Data Bases (VLDB)
, pp. 325-336
-
-
Kim, M.-S.1
Whang, K.-Y.2
Lee, J.-G.3
Lee, M.-J.4
-
19
-
-
23444433057
-
miblast: scalable evaluation of a batch of nucleotide sequence queries with blast
-
Y. J. Kim, A. Boyd, B. D. Athey, and J. M. Patel. miblast: scalable evaluation of a batch of nucleotide sequence queries with blast. Nucleic Acids Res, 33:4335-4344, 2005.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 4335-4344
-
-
Kim, Y.J.1
Boyd, A.2
Athey, B.D.3
Patel, J.M.4
-
20
-
-
0003352252
-
The art of computer programming
-
D. E. Knuth. The art of computer programming. Sorting and Searching, 3, 1973.
-
(1973)
Sorting and Searching
, vol.3
-
-
Knuth, D.E.1
-
21
-
-
0034519012
-
Mpblast : improved blast performance with multiplexed queries
-
I. Korf and W. Gish. Mpblast : improved blast performance with multiplexed queries. Bioinformatics, 16:1052-1053, 2000.
-
(2000)
Bioinformatics
, vol.16
, pp. 1052-1053
-
-
Korf, I.1
Gish, W.2
-
22
-
-
40749108125
-
Compressed indexing and local alignment of dna
-
T. W. Lam, W. K. Sung, S. L. Tam, C. Wong, and S. Yiu. Compressed indexing and local alignment of dna. Bioinformatics, 24(6), 2008.
-
(2008)
Bioinformatics
, vol.24
, Issue.6
-
-
Lam, T.W.1
Sung, W.K.2
Tam, S.L.3
Wong, C.4
Yiu, S.5
-
23
-
-
0001116877
-
Binary codes capable of correcting deletions, insertions, and reversals
-
V. I. Levenshtein. Binary codes capable of correcting deletions, insertions, and reversals. Soviet Physics, 10(8):707-710, 1966.
-
(1966)
Soviet Physics
, vol.10
, Issue.8
, pp. 707-710
-
-
Levenshtein, V.I.1
-
25
-
-
85011032600
-
improving performance of approximate queries on string collections using variable-length grams
-
C. Li, B. Wang, and X. Yang. Vgram: improving performance of approximate queries on string collections using variable-length grams. In International Conference on Very Large Data Bases (VLDB), pages 303-314, 2007.
-
(2007)
International Conference on Very Large Data Bases (VLDB)
, pp. 303-314
-
-
Li, C.1
Wang, B.2
Yang, X.3
-
26
-
-
0021919480
-
Rapid and sensitive protein similarity searches
-
March
-
D. J. Lipman and W. R. Pearson. Rapid and sensitive protein similarity searches. Science, 227(4693):1435-1441, March 1985.
-
(1985)
Science
, vol.227
, Issue.4693
, pp. 1435-1441
-
-
Lipman, D.J.1
Pearson, W.R.2
-
27
-
-
85011115146
-
Fast ngram-based string search over data encoded using algebraic signatures
-
W. Litwin, R. Mokadem, P. Rigaux, and T. Schwarz. Fast ngram-based string search over data encoded using algebraic signatures. In International Conference on Very Large Data Bases (VLDB), pages 207-218, 2007.
-
(2007)
International Conference on Very Large Data Bases (VLDB)
, pp. 207-218
-
-
Litwin, W.1
Mokadem, R.2
Rigaux, P.3
Schwarz, T.4
-
31
-
-
84937439801
-
Indexing text with approximate q-grams
-
C. Navarro, E. Sutinen, J. Tanninen, and J. Tarhio. Indexing text with approximate q-grams. In COM '00: Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching, pages 350-363, 2000.
-
(2000)
COM '00: Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
, pp. 350-363
-
-
Navarro, C.1
Sutinen, E.2
Tanninen, J.3
Tarhio, J.4
-
32
-
-
84957654004
-
A new indexing method for approximate string matching
-
G. Navarro and R. Baeza-Yates. A new indexing method for approximate string matching. In Combinatorial Pattern Matching, 10th Annual Symposium, pages 163-185, 1999.
-
(1999)
Combinatorial Pattern Matching
, pp. 163-185
-
-
Navarro, G.1
Baeza-Yates, R.2
-
33
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
S. Needleman and C. Wunsch. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal on Molecular Biology, 48(3):443-53, 1970.
-
(1970)
Journal on Molecular Biology
, vol.48
, Issue.3
, pp. 443-453
-
-
Needleman, S.1
Wunsch, C.2
-
34
-
-
0034764307
-
SSAHA: A fast search method for large dna databases
-
Z. Ning, A. J. Cox, and J. C. Mullikin. SSAHA: A fast search method for large dna databases. Genome Resources, 11(10):1725-1729, 2001.
-
(2001)
Genome Resources
, vol.11
, Issue.10
, pp. 1725-1729
-
-
Ning, Z.1
Cox, A.J.2
Mullikin, J.C.3
-
35
-
-
0023989064
-
Improved tools for biological sequence comparison
-
April
-
W. R. Pearson and D. J. Lipman. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A, 85(8):2444-2448, April 1988.
-
(1988)
Proc Natl Acad Sci U S A
, vol.85
, Issue.8
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
38
-
-
0017334283
-
Similarity of the general designs of protochordates and invertebrates
-
G. J. Russell and J. H. Subak-Sharpe. Similarity of the general designs of protochordates and invertebrates. Nature, 266:533-536, 1977.
-
(1977)
Nature
, vol.266
, pp. 533-536
-
-
Russell, G.J.1
Subak-Sharpe, J.H.2
-
39
-
-
0019887799
-
Identification of common molecular subsequences
-
T. F. Smith and M. S. Waterman. Identification of common molecular subsequences. Journal of Molecular Biology, 147:195-197, 1981.
-
(1981)
Journal of Molecular Biology
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
40
-
-
0020494998
-
Algorithms for approximate string matching
-
E. Ukkonen. Algorithms for approximate string matching. Information Control, 64(1-3):100-118, 1985.
-
(1985)
Information Control
, vol.64
, Issue.1-3
, pp. 100-118
-
-
Ukkonen, E.1
-
41
-
-
0001704377
-
On-line construction of suffix trees
-
E. Ukkonen. On-line construction of suffix trees. Algorithmica, 14(3):249-260, 1995.
-
(1995)
Algorithmica
, vol.14
, Issue.3
, pp. 249-260
-
-
Ukkonen, E.1
-
42
-
-
84939567221
-
Reference-based indexing of sequence databases
-
J. Venkateswaran, D. Lachwani, T. Kahveci, and C. Jermaine. Reference-based indexing of sequence databases. In International Conference on Very Large Databases (VLDB), pages 906-917, 2006.
-
(2006)
International Conference on Very Large Databases (VLDB)
, pp. 906-917
-
-
Venkateswaran, J.1
Lachwani, D.2
Kahveci, T.3
Jermaine, C.4
-
43
-
-
57149130672
-
Cost-based variable-length-gram selection for string collections to support approximate queries efficiently
-
X. Yang, B. Wang, and C. Li. Cost-based variable-length-gram selection for string collections to support approximate queries efficiently. In ACM International Conference on Management Of Data (SIGMOD), pages 353-364, 2008.
-
(2008)
ACM International Conference on Management Of Data (SIGMOD)
, pp. 353-364
-
-
Yang, X.1
Wang, B.2
Li, C.3
-
44
-
-
0034053725
-
A greedy algorithm for aligning dna sequences
-
Z. Zhang, S. Schwartz, L. Wagner, and W. Miller. A greedy algorithm for aligning dna sequences. Journal of Computational Biology, 7:203-214, 2000.
-
(2000)
Journal of Computational Biology
, vol.7
, pp. 203-214
-
-
Zhang, Z.1
Schwartz, S.2
Wagner, L.3
Miller, W.4
|