Spaced seed (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Spaced seed" in English language version.

refsWebsite

Global rank English rank

18nih.gov

4^th place

16doi.org

2^nd place

4worldcat.org

5^th place

3semanticscholar.org

11^th place

8^th place

2harvard.edu

18^th place

17^th place

1arxiv.org

69^th place

59^th place

1oup.com

485^th place

440^th place

arxiv.org

Břinda, Karel; Sykulski, Maciej; Kucherov, Gregory (November 2015). "Spaced seeds improve k-mer-based metagenomic classification". Bioinformatics. 31 (22): 3584–3592. arXiv:1502.06256. Bibcode:2015Bioin..31.3584B. doi:10.1093/bioinformatics/btv419. PMID 26209798.

doi.org

Ma, Bin; Tromp, John; Li, Ming (March 2002). "PatternHunter: faster and more sensitive homology search". Bioinformatics. 18 (3): 440–445. doi:10.1093/bioinformatics/18.3.440. PMID 11934743.
David, Matei; Dzamba, Misko; Lister, Dan; Ilie, Lucian; Brudno, Michael (April 2011). "SHRiMP2: Sensitive yet Practical Short Read Mapping". Bioinformatics. 27 (7): 1011–1012. doi:10.1093/bioinformatics/btr046. PMID 21278192.
Birol, I; Chu, J; Mohamadi, H; Jackman, S. D.; Raghavan, K; Vandervalk, B. P.; Raymond, A; Warren, René L. (2015). "Spaced Seed Data Structures for De Novo Assembly". International Journal of Genomics. 2015: 196591. doi:10.1155/2015/196591. PMC 4619942. PMID 26539459.
Břinda, Karel; Sykulski, Maciej; Kucherov, Gregory (November 2015). "Spaced seeds improve k-mer-based metagenomic classification". Bioinformatics. 31 (22): 3584–3592. arXiv:1502.06256. Bibcode:2015Bioin..31.3584B. doi:10.1093/bioinformatics/btv419. PMID 26209798.
Auton, A.; Brooks, L. D.; Durbin, R. M.; Garrison, E. P.; Kang, H. M.; Korbel, J. O.; Marchini, J. L.; McCarthy, S.; McVean, G. A.; Abecasis, G. R.; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Green, Eric D.; Hurles, Matthew E.; Knoppers, Bartha M.; Korbel, Jan O.; Lander, Eric S.; Lee, Charles; Lehrach, Hans; Mardis, Elaine R.; Marth, Gabor T.; McVean, Gil A.; Nickerson, Deborah A.; Schmidt, Jeanette P.; Sherry, Stephen T.; Wang, Jun; Gibbs, Richard A.; Boerwinkle, Eric; et al. (2015-10-01). "A global reference for human genetic variation". Nature. 526 (7571): 68–74. Bibcode:2015Natur.526...68T. doi:10.1038/nature15393. ISSN 0028-0836. PMC 4750478. PMID 26432245.
Califano, A.; Rigoutsos, I. (1993). "FLASH: A fast look-up algorithm for string homology". Proceedings of IEEE Conference on Computer Vision and Pattern Recognition. Vol. 1. pp. 353–359. doi:10.1109/CVPR.1993.341106. ISBN 0-8186-3880-X. PMID 7584371. S2CID 2862905.
Pevzner, P.A.; Waterman, M.S. (1995). "Multiple filtration and approximate pattern matching". Algorithmica. 13 (1–2): 135–154. doi:10.1007/BF01188584. S2CID 10243441.
Burkhardt, Stefan; Kärkkäinen, Juha (June 2001). "Better Filtering with Gapped q-Grams". Combinatorial Pattern Matching. Lecture Notes in Computer Science. Vol. 2089. pp. 73–85. doi:10.1007/3-540-48194-X_6. ISBN 978-3-540-42271-6.
Li, Ming; Ma, Bin; Kisman, Derek; Tromp, John (2003). "PatternHunter II: Highly Sensitive and Fast Homology Search". Genome Informatics. 14: 164–175. doi:10.11234/gi1990.14.164. PMID 15706531.
Gotea, Valer; Veeramachaneni, Vamsi; Makałowski, Wojciech (2003-12-01). "Mastering seeds for genomic size nucleotide BLAST searches". Nucleic Acids Research. 31 (23): 6935–6941. doi:10.1093/nar/gkg886. ISSN 0305-1048. PMC 290255. PMID 14627826.
Altschul, Stephen F.; Gish, Warren; Miller, Webb; Myers, Eugene W.; Lipman, David J. (15 May 1990). "Basic local alignment search tool". Journal of Molecular Biology. 215 (3): 403–410. doi:10.1016/S0022-2836(05)80360-2. PMID 2231712. S2CID 14441902.
Li, Heng (15 September 2018). "Minimap2: pairwise alignment for nucleotide sequences". Bioinformatics. 34 (18): 3094–3100. doi:10.1093/bioinformatics/bty191. PMC 6137996. PMID 29750242.
Langmead, B.; Salzberg, S. (2012). "Fast gapped-read alignment with Bowtie 2". Nature Methods. 9 (4): 357–359. doi:10.1038/nmeth.1923. PMC 3322381. PMID 22388286.
Choi, Kwok Pui; Zhang, Louxin (2004-02-01). "Sensitivity analysis and efficient method for identifying optimal spaced seeds". Journal of Computer and System Sciences. 68 (1): 22–40. doi:10.1016/j.jcss.2003.04.002. ISSN 0022-0000.
Kong, Yong (2007-03-01). "Generalized Correlation Functions and Their Applications in Selection of Optimal Multiple Spaced Seeds for Homology Search". Journal of Computational Biology. 14 (2): 238–254. doi:10.1089/cmb.2006.0008. PMID 17456017.
Ilie, Lucian; Ilie, Silvana (2007-11-15). "Multiple spaced seeds for homology search". Bioinformatics. 23 (22): 2969–2977. doi:10.1093/bioinformatics/btm422. ISSN 1367-4803. PMID 17804438.

harvard.edu

ui.adsabs.harvard.edu

Břinda, Karel; Sykulski, Maciej; Kucherov, Gregory (November 2015). "Spaced seeds improve k-mer-based metagenomic classification". Bioinformatics. 31 (22): 3584–3592. arXiv:1502.06256. Bibcode:2015Bioin..31.3584B. doi:10.1093/bioinformatics/btv419. PMID 26209798.
Auton, A.; Brooks, L. D.; Durbin, R. M.; Garrison, E. P.; Kang, H. M.; Korbel, J. O.; Marchini, J. L.; McCarthy, S.; McVean, G. A.; Abecasis, G. R.; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Green, Eric D.; Hurles, Matthew E.; Knoppers, Bartha M.; Korbel, Jan O.; Lander, Eric S.; Lee, Charles; Lehrach, Hans; Mardis, Elaine R.; Marth, Gabor T.; McVean, Gil A.; Nickerson, Deborah A.; Schmidt, Jeanette P.; Sherry, Stephen T.; Wang, Jun; Gibbs, Richard A.; Boerwinkle, Eric; et al. (2015-10-01). "A global reference for human genetic variation". Nature. 526 (7571): 68–74. Bibcode:2015Natur.526...68T. doi:10.1038/nature15393. ISSN 0028-0836. PMC 4750478. PMID 26432245.

nih.gov

pubmed.ncbi.nlm.nih.gov

Ma, Bin; Tromp, John; Li, Ming (March 2002). "PatternHunter: faster and more sensitive homology search". Bioinformatics. 18 (3): 440–445. doi:10.1093/bioinformatics/18.3.440. PMID 11934743.
David, Matei; Dzamba, Misko; Lister, Dan; Ilie, Lucian; Brudno, Michael (April 2011). "SHRiMP2: Sensitive yet Practical Short Read Mapping". Bioinformatics. 27 (7): 1011–1012. doi:10.1093/bioinformatics/btr046. PMID 21278192.
Birol, I; Chu, J; Mohamadi, H; Jackman, S. D.; Raghavan, K; Vandervalk, B. P.; Raymond, A; Warren, René L. (2015). "Spaced Seed Data Structures for De Novo Assembly". International Journal of Genomics. 2015: 196591. doi:10.1155/2015/196591. PMC 4619942. PMID 26539459.
Břinda, Karel; Sykulski, Maciej; Kucherov, Gregory (November 2015). "Spaced seeds improve k-mer-based metagenomic classification". Bioinformatics. 31 (22): 3584–3592. arXiv:1502.06256. Bibcode:2015Bioin..31.3584B. doi:10.1093/bioinformatics/btv419. PMID 26209798.
Auton, A.; Brooks, L. D.; Durbin, R. M.; Garrison, E. P.; Kang, H. M.; Korbel, J. O.; Marchini, J. L.; McCarthy, S.; McVean, G. A.; Abecasis, G. R.; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Green, Eric D.; Hurles, Matthew E.; Knoppers, Bartha M.; Korbel, Jan O.; Lander, Eric S.; Lee, Charles; Lehrach, Hans; Mardis, Elaine R.; Marth, Gabor T.; McVean, Gil A.; Nickerson, Deborah A.; Schmidt, Jeanette P.; Sherry, Stephen T.; Wang, Jun; Gibbs, Richard A.; Boerwinkle, Eric; et al. (2015-10-01). "A global reference for human genetic variation". Nature. 526 (7571): 68–74. Bibcode:2015Natur.526...68T. doi:10.1038/nature15393. ISSN 0028-0836. PMC 4750478. PMID 26432245.
Califano, A.; Rigoutsos, I. (1993). "FLASH: A fast look-up algorithm for string homology". Proceedings of IEEE Conference on Computer Vision and Pattern Recognition. Vol. 1. pp. 353–359. doi:10.1109/CVPR.1993.341106. ISBN 0-8186-3880-X. PMID 7584371. S2CID 2862905.
Li, Ming; Ma, Bin; Kisman, Derek; Tromp, John (2003). "PatternHunter II: Highly Sensitive and Fast Homology Search". Genome Informatics. 14: 164–175. doi:10.11234/gi1990.14.164. PMID 15706531.
Gotea, Valer; Veeramachaneni, Vamsi; Makałowski, Wojciech (2003-12-01). "Mastering seeds for genomic size nucleotide BLAST searches". Nucleic Acids Research. 31 (23): 6935–6941. doi:10.1093/nar/gkg886. ISSN 0305-1048. PMC 290255. PMID 14627826.
Altschul, Stephen F.; Gish, Warren; Miller, Webb; Myers, Eugene W.; Lipman, David J. (15 May 1990). "Basic local alignment search tool". Journal of Molecular Biology. 215 (3): 403–410. doi:10.1016/S0022-2836(05)80360-2. PMID 2231712. S2CID 14441902.
Li, Heng (15 September 2018). "Minimap2: pairwise alignment for nucleotide sequences". Bioinformatics. 34 (18): 3094–3100. doi:10.1093/bioinformatics/bty191. PMC 6137996. PMID 29750242.
Langmead, B.; Salzberg, S. (2012). "Fast gapped-read alignment with Bowtie 2". Nature Methods. 9 (4): 357–359. doi:10.1038/nmeth.1923. PMC 3322381. PMID 22388286.
Kong, Yong (2007-03-01). "Generalized Correlation Functions and Their Applications in Selection of Optimal Multiple Spaced Seeds for Homology Search". Journal of Computational Biology. 14 (2): 238–254. doi:10.1089/cmb.2006.0008. PMID 17456017.
Ilie, Lucian; Ilie, Silvana (2007-11-15). "Multiple spaced seeds for homology search". Bioinformatics. 23 (22): 2969–2977. doi:10.1093/bioinformatics/btm422. ISSN 1367-4803. PMID 17804438.

ncbi.nlm.nih.gov

Birol, I; Chu, J; Mohamadi, H; Jackman, S. D.; Raghavan, K; Vandervalk, B. P.; Raymond, A; Warren, René L. (2015). "Spaced Seed Data Structures for De Novo Assembly". International Journal of Genomics. 2015: 196591. doi:10.1155/2015/196591. PMC 4619942. PMID 26539459.
Auton, A.; Brooks, L. D.; Durbin, R. M.; Garrison, E. P.; Kang, H. M.; Korbel, J. O.; Marchini, J. L.; McCarthy, S.; McVean, G. A.; Abecasis, G. R.; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Green, Eric D.; Hurles, Matthew E.; Knoppers, Bartha M.; Korbel, Jan O.; Lander, Eric S.; Lee, Charles; Lehrach, Hans; Mardis, Elaine R.; Marth, Gabor T.; McVean, Gil A.; Nickerson, Deborah A.; Schmidt, Jeanette P.; Sherry, Stephen T.; Wang, Jun; Gibbs, Richard A.; Boerwinkle, Eric; et al. (2015-10-01). "A global reference for human genetic variation". Nature. 526 (7571): 68–74. Bibcode:2015Natur.526...68T. doi:10.1038/nature15393. ISSN 0028-0836. PMC 4750478. PMID 26432245.
Gotea, Valer; Veeramachaneni, Vamsi; Makałowski, Wojciech (2003-12-01). "Mastering seeds for genomic size nucleotide BLAST searches". Nucleic Acids Research. 31 (23): 6935–6941. doi:10.1093/nar/gkg886. ISSN 0305-1048. PMC 290255. PMID 14627826.
Li, Heng (15 September 2018). "Minimap2: pairwise alignment for nucleotide sequences". Bioinformatics. 34 (18): 3094–3100. doi:10.1093/bioinformatics/bty191. PMC 6137996. PMID 29750242.
Langmead, B.; Salzberg, S. (2012). "Fast gapped-read alignment with Bowtie 2". Nature Methods. 9 (4): 357–359. doi:10.1038/nmeth.1923. PMC 3322381. PMID 22388286.

oup.com

academic.oup.com

Ilie, Lucian; Ilie, Silvana (2007-11-15). "Multiple spaced seeds for homology search". Bioinformatics. 23 (22): 2969–2977. doi:10.1093/bioinformatics/btm422. ISSN 1367-4803. PMID 17804438.

semanticscholar.org

api.semanticscholar.org

Califano, A.; Rigoutsos, I. (1993). "FLASH: A fast look-up algorithm for string homology". Proceedings of IEEE Conference on Computer Vision and Pattern Recognition. Vol. 1. pp. 353–359. doi:10.1109/CVPR.1993.341106. ISBN 0-8186-3880-X. PMID 7584371. S2CID 2862905.
Pevzner, P.A.; Waterman, M.S. (1995). "Multiple filtration and approximate pattern matching". Algorithmica. 13 (1–2): 135–154. doi:10.1007/BF01188584. S2CID 10243441.
Altschul, Stephen F.; Gish, Warren; Miller, Webb; Myers, Eugene W.; Lipman, David J. (15 May 1990). "Basic local alignment search tool". Journal of Molecular Biology. 215 (3): 403–410. doi:10.1016/S0022-2836(05)80360-2. PMID 2231712. S2CID 14441902.

worldcat.org

search.worldcat.org

Auton, A.; Brooks, L. D.; Durbin, R. M.; Garrison, E. P.; Kang, H. M.; Korbel, J. O.; Marchini, J. L.; McCarthy, S.; McVean, G. A.; Abecasis, G. R.; Flicek, Paul; Gabriel, Stacey B.; Gibbs, Richard A.; Green, Eric D.; Hurles, Matthew E.; Knoppers, Bartha M.; Korbel, Jan O.; Lander, Eric S.; Lee, Charles; Lehrach, Hans; Mardis, Elaine R.; Marth, Gabor T.; McVean, Gil A.; Nickerson, Deborah A.; Schmidt, Jeanette P.; Sherry, Stephen T.; Wang, Jun; Gibbs, Richard A.; Boerwinkle, Eric; et al. (2015-10-01). "A global reference for human genetic variation". Nature. 526 (7571): 68–74. Bibcode:2015Natur.526...68T. doi:10.1038/nature15393. ISSN 0028-0836. PMC 4750478. PMID 26432245.
Gotea, Valer; Veeramachaneni, Vamsi; Makałowski, Wojciech (2003-12-01). "Mastering seeds for genomic size nucleotide BLAST searches". Nucleic Acids Research. 31 (23): 6935–6941. doi:10.1093/nar/gkg886. ISSN 0305-1048. PMC 290255. PMID 14627826.
Choi, Kwok Pui; Zhang, Louxin (2004-02-01). "Sensitivity analysis and efficient method for identifying optimal spaced seeds". Journal of Computer and System Sciences. 68 (1): 22–40. doi:10.1016/j.jcss.2003.04.002. ISSN 0022-0000.
Ilie, Lucian; Ilie, Silvana (2007-11-15). "Multiple spaced seeds for homology search". Bioinformatics. 23 (22): 2969–2977. doi:10.1093/bioinformatics/btm422. ISSN 1367-4803. PMID 17804438.