Academic Journal
Multiseed Lossless Filtration
| Τίτλος: | Multiseed Lossless Filtration |
|---|---|
| Συγγραφείς: | Kucherov, Gregory, Noé, Laurent, Roytberg, Mikhail |
| Συνεισφορές: | Kucherov, Gregory, Laboratoire d'Informatique Fondamentale de Lille (LIFL), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS), Sequential Learning (SEQUOIA), Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lille, Sciences Humaines et Sociales-Centre National de la Recherche Scientifique (CNRS)-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria), Institute of Mathematical Problems in Biology (IMPB RAS), Russian Academy of Sciences Moscow (RAS) |
| Πηγή: | Lecture Notes in Computer Science ISBN: 9783540223412 |
| Publication Status: | Preprint |
| Στοιχεία εκδότη: | Institute of Electrical and Electronics Engineers (IEEE), 2004. |
| Έτος έκδοσης: | 2004 |
| Θεματικοί όροι: | string matching, Molecular Sequence Data, 0206 medical engineering, [INFO.INFO-DS] Computer Science [cs]/Data Structures and Algorithms [cs.DS], 0102 computer and information sciences, 02 engineering and technology, seed family, Quantitative Biology - Quantitative Methods, 01 natural sciences, Sequence Homology, Nucleic Acid, Quantitative Methods (q-bio.QM), [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], filtration, dynamic programming, Expressed Sequence Tags, gapped q-gram, Base Sequence, oligonucleotide selection, ACM: F.: Theory of Computation/F.2: ANALYSIS OF ALGORITHMS AND PROBLEM COMPLEXITY/F.2.2: Nonnumerical Algorithms and Problems/F.2.2.3: Pattern matching, local alignment, Sequence Analysis, DNA, ACM: G.: Mathematics of Computing/G.2: DISCRETE MATHEMATICS/G.2.3: Applications, sequence similarity, multiple spaced seeds, FOS: Biological sciences, est, ACM: J.: Computer Applications/J.3: LIFE AND MEDICAL SCIENCES/J.3.0: Biology and genetics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], gapped seed, Sequence Alignment, Algorithms |
| Περιγραφή: | We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed as studied by Burkhardt and K��rkk��inen [1]. We present algorithms to compute several important parameters of seed families, study their combinatorial properties, and describe several techniques to construct efficient families. We also report a large-scale application of the proposed technique to the problem of oligonucleotide selection for an EST sequence database. |
| Τύπος εγγράφου: | Article Part of book or chapter of book |
| Περιγραφή αρχείου: | application/pdf |
| Γλώσσα: | English |
| ISSN: | 1545-5963 |
| DOI: | 10.1109/tcbb.2005.12 |
| DOI: | 10.1007/978-3-540-27801-6_22 |
| DOI: | 10.48550/arxiv.0901.3215 |
| Σύνδεσμος πρόσβασης: | http://arxiv.org/pdf/0901.3215 https://hal.inria.fr/inria-00354810/file/KucherovNoeRoytberg.pdf https://pubmed.ncbi.nlm.nih.gov/17044164 http://arxiv.org/abs/0901.3215 https://inria.hal.science/inria-00000718v1 https://doi.org/10.1109/tcbb.2005.12 https://inria.hal.science/inria-00354810v1 https://inria.hal.science/inria-00354810v1/document https://doi.org/10.1109/tcbb.2005.12 https://rd.springer.com/chapter/10.1007/978-3-540-27801-6_22 https://link.springer.com/chapter/10.1007/978-3-540-27801-6_22 http://ui.adsabs.harvard.edu/abs/2009arXiv0901.3215K/abstract https://dl.acm.org/doi/10.1109/TCBB.2005.12 http://ieeexplore.ieee.org/document/1416851/ https://ieeexplore.ieee.org/document/1416851/ http://export.arxiv.org/pdf/0901.3215 http://www.ncbi.nlm.nih.gov/pubmed/17044164 |
| Rights: | IEEE Copyright arXiv Non-Exclusive Distribution |
| Αριθμός Καταχώρησης: | edsair.doi.dedup.....2eceae7dd054d2667867e84a2a6e6c82 |
| Βάση Δεδομένων: | OpenAIRE |
| ISSN: | 15455963 |
|---|---|
| DOI: | 10.1109/tcbb.2005.12 |