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1. WO2006096324 - METHOD AND APPARATUS FOR PERFORMING BIOSEQUENCE SIMILARITY SEARCHING

Publication Number WO/2006/096324
Publication Date 14.09.2006
International Application No. PCT/US2006/006105
International Filing Date 22.02.2006
IPC
G06F 17/30 2006.01
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
FELECTRIC DIGITAL DATA PROCESSING
17Digital computing or data processing equipment or methods, specially adapted for specific functions
30Information retrieval; Database structures therefor
G06F 19/22 2011.01
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
FELECTRIC DIGITAL DATA PROCESSING
19Digital computing or data processing equipment or methods, specially adapted for specific applications
10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
22for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism discovery or sequence alignment
G06F 19/28 2011.01
GPHYSICS
06COMPUTING; CALCULATING OR COUNTING
FELECTRIC DIGITAL DATA PROCESSING
19Digital computing or data processing equipment or methods, specially adapted for specific applications
10Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
28for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
CPC
G06F 16/2255
GPHYSICS
06COMPUTING; CALCULATING; COUNTING
FELECTRIC DIGITAL DATA PROCESSING
16Information retrieval; Database structures therefor; File system structures therefor
20of structured data, e.g. relational data
22Indexing; Data structures therefor; Storage structures
2228Indexing structures
2255Hash tables
G16B 30/00
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
30ICT specially adapted for sequence analysis involving nucleotides or amino acids
G16B 50/00
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
50ICT programming tools or database systems specially adapted for bioinformatics
Applicants
  • WASHINGTON UNIVERSITY [US]/[US] (AE, AG, AL, AM, AT, AU, AZ, BA, BB, BE, BF, BG, BJ, BR, BW, BY, BZ, CA, CF, CG, CH, CI, CM, CN, CO, CR, CU, CY, CZ, DE, DK, DM, DZ, EC, EE, EG, ES, FI, FR, GA, GB, GD, GE, GH, GM, GN, GQ, GR, GW, HR, HU, ID, IE, IL, IN, IS, IT, JP, KE, KG, KM, KN, KP, KR, KZ, LC, LK, LR, LS, LT, LU, LV, LY, MA, MC, MD, MG, MK, ML, MN, MR, MW, MX, MZ, NA, NE, NG, NI, NL, NO, NZ, OM, PG, PH, PL, PT, RO, RU, SC, SD, SE, SG, SI, SK, SL, SM, SN, SY, SZ, TD, TG, TJ, TM, TN, TR, TT, TZ, UA, UG, UZ, VC, VN, YU, ZA, ZM, ZW)
  • BUHLER, Jeremy Daniel [US]/[US] (UsOnly)
  • CHAMBERLAIN, Roger Dean [US]/[US] (UsOnly)
  • FRANKLIN, Mark Allen [US]/[US] (UsOnly)
  • GYANG, Kwame [GH]/[US] (UsOnly)
  • JACOB, Arpith Chacko [IN]/[US] (UsOnly)
  • KRISHNAMURTHY, Praveen [IN]/[US] (UsOnly)
  • LANCASTER, Joseph Marion [US]/[US] (UsOnly)
Inventors
  • BUHLER, Jeremy Daniel
  • CHAMBERLAIN, Roger Dean
  • FRANKLIN, Mark Allen
  • GYANG, Kwame
  • JACOB, Arpith Chacko
  • KRISHNAMURTHY, Praveen
  • LANCASTER, Joseph Marion
Agents
  • KERCHER, Kevin M.
Priority Data
60/658,41803.03.2005US
60/736,08111.11.2005US
Publication Language English (EN)
Filing Language English (EN)
Designated States
Title
(EN) METHOD AND APPARATUS FOR PERFORMING BIOSEQUENCE SIMILARITY SEARCHING
(FR) PROCEDE ET APPAREIL PERMETTANT D'EFFECTUER UNE RECHERCHE DE SIMILARITE DE SEQUENCES BIOLOGIQUES
Abstract
(EN)
A system and method for performing biological sequence similarity searching is disclosed. This includes a programmable logic device configured to include a pipeline that comprises a matching stage, the matching stage being configured to receive a data stream comprising a plurality of possible matches between a plurality of biological sequence data strings and a plurality of substrings of a query string. The pipeline may further include a ungapped extension prefilter stage located downstream from the matching stage, the prefilter stage being configured to shift through pattern matches between the biological sequence data strings and the plurality of substrings of a query string and provide a score so that only pattern matches that exceed a user defined score will pass downstream from the prefilter stage. The matching stage may include at least one Bloom filter.
(FR)
La présente invention se rapporte à un système et à un procédé permettant d'effectuer une recherche de similarité de séquences biologiques. Le système selon l'invention comprend un dispositif logique programmable, configuré pour comporter un pipeline possédant un étage d'appariement, ce dernier étant adapté pour recevoir un flux de données renfermant une pluralité de concordances possibles entre une pluralité de chaînes de données de séquences biologiques et une pluralité de sous-chaînes d'une chaîne de requête. Le pipeline peut également comprendre un étage de préfiltrage d'extension sans indels, situé en aval de l'étage d'appariement, l'étage de préfiltrage étant adapté pour passer en revue les concordances de formes entre les chaînes de données de séquences biologiques et la pluralité de sous-chaînes d'une chaîne de requête, et pour fournir un score tel que seules les concordances de formes qui dépassent un score défini par l'utilisateur passeront en aval de l'étage de préfiltrage. L'étage d'appariement peut comporter au moins un filtre Bloom.
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