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1. 发明专利

IL265928D0 Method and systems for the representation and processing of bioinformatics data using reference sequences 未知
公开(公告)号：IL265928D0
公开(公告)日：2019-05-30
申请号：IL26592819
申请日：2019-04-08
申请人： GENOMSYS SA , ALBERTI CLAUDIO , ZOIA GIORGIO , RENZI DANIELE , BALUCH MOHAMED KHOSO
发明人： ALBERTI CLAUDIO , ZOIA GIORGIO , RENZI DANIELE , BALUCH MOHAMED KHOSO
IPC分类号： C40B20060101 , G16B45/00
摘要： Method and apparatus for the compression of genome sequence data produced by genome sequencing machines. Sequence reads are coded by aligning them with respect to pre-existing or constructed reference sequences, the coding process is composed of a classification of the reads into data classes followed by the coding of each class in terms of a multiplicity of genomic descriptors. Genomic descriptors of the same type are organized in blocks which are compressed by applying successive transformation stages, binarization and entropy coding. Specific source models and entropy coders are used for each data class and for each associated descriptor.

2. 发明专利

IL265928A Method and systems for the representation and processing of bioinformatics data using reference sequences 未知
公开(公告)号：IL265928A
公开(公告)日：2020-10-29
申请号：IL26592819
申请日：2019-04-08
申请人： GENOMSYS SA , ALBERTI CLAUDIO , ZOIA GIORGIO , RENZI DANIELE , BALUCH MOHAMED KHOSO
发明人： ALBERTI CLAUDIO , ZOIA GIORGIO , RENZI DANIELE , BALUCH MOHAMED KHOSO
IPC分类号： G06F3/048 , G06F7/00 , G06F16/22 , G06F16/23 , G06F16/28 , G06F21/60 , G06F21/62 , G16B20/10 , G16B20/20 , G16B30/00 , G16B30/10 , G16B30/20 , G16B40/00 , G16B40/10 , G16B45/00 , G16B50/10 , G16B50/30 , G16B50/40 , G16B50/50 , G16B99/00 , H03M7/30
摘要： Method and apparatus for the compression of genome sequence data produced by genome sequencing machines. Sequence reads are coded by aligning them with respect to pre-existing or constructed reference sequences, the coding process is composed of a classification of the reads into data classes followed by the coding of each class in terms of a multiplicity of genomic descriptors. Genomic descriptors of the same type are organized in blocks which are compressed by applying successive transformation stages, binarization and entropy coding. Specific source models and entropy coders are used for each data class and for each associated descriptor.

3. 发明专利

IL265956D0 Method and apparatus for the access to bioinformatics data structured in access units 未知
公开(公告)号：IL265956D0
公开(公告)日：2019-05-30
申请号：IL26595619
申请日：2019-04-10
申请人： GENOMSYS SA , ALBERTI CLAUDIO , ZOIA GIORGIO , RENZI DANIELE , BALUCH MOHAMED KHOSO
发明人： ALBERTI CLAUDIO , ZOIA GIORGIO , RENZI DANIELE , BALUCH MOHAMED KHOSO
IPC分类号： G16B45/00
摘要： Method and apparatus for the coding and selective access of compressed genomic sequence data produced by genomic sequencing machines. The coding process is based on aligning sequence reads with respect to pre-existing or constructed reference sequences, on classifying and coding the sequence reads by means of sets of descriptors, and further partitioning the descriptor sets into access units of different types. Efficient selective access to specific genomic regions with the guarantee of retrieving all sequence reads mapped to those regions, is provided by: signaling the type of data mapping configuration used to store or transmit the descriptor sets, determining the minimum number of access units that need to be retrieved and decoded to access a genomic region, providing a master index table that contain all information for optimizing the data access process.

4. 发明专利

IL265879D0 Method and systems for the indexing of bioinformatics data 未知
公开(公告)号：IL265879D0
公开(公告)日：2019-06-30
申请号：IL26587919
申请日：2019-04-07
申请人： GENOMSYS SA , ALBERTI CLAUDIO , ZOIA GIORGIO , RENZI DANIELE , BALUCH MOHAMED KHOSO
发明人： ALBERTI CLAUDIO , ZOIA GIORGIO , RENZI DANIELE , BALUCH MOHAMED KHOSO
IPC分类号： G16B20190101 , G16B45/00
摘要： Method and apparatus for the compression of genome sequence data produced by genome sequencing machines. Sequence reads are coded by aligning them with respect to pre-existing or constructed reference sequences, the coding process is composed of a classification of the reads into data classes followed by the coding of each class in terms of a multiplicity of genomic descriptors. Genomic descriptors of the same type are organized in blocks which are compressed by applying successive transformation stages, binarization and entropy coding. Specific source models and entropy coders are used for each data class and for each associated descriptor.

5. 发明专利

IL265972D0 Method and system for selective access of stored or transmitted bioinformatics data 未知
公开(公告)号：IL265972D0
公开(公告)日：2019-06-30
申请号：IL26597219
申请日：2019-04-11
申请人： GENOMSYS SA , ZOIA GIORGIO , RENZI DANIELE , BALUCH MOHAMED KHOSO
发明人： ZOIA GIORGIO , RENZI DANIELE , BALUCH MOHAMED KHOSO
IPC分类号： G16B20190101 , G16B45/00
摘要： Method and apparatus for the compression of genome sequence data produced by genome sequencing machines. Sequence reads are coded by aligning them with respect to pre-existing or constructed reference sequences, the coding process is composed of a classification of the reads into data classes followed by the coding of each class in terms of a multiplicity of genomic descriptors. Genomic descriptors of the same type are organized in blocks which are compressed by applying successive transformation stages, binarization and entropy coding. Specific source models and entropy coders are used for each data class and for each associated descriptor.

6. 发明专利

PH12019501880A1 METHOD AND SYSTEMS FOR THE RECONSTRUCTION OF GENOMIC REFERENCE SEQUENCES FROM COMPRESSED GENOMIC SEQUENCE READS 未知
公开(公告)号：PH12019501880A1
公开(公告)日：2020-06-29
申请号：PH12019501880
申请日：2019-08-13
申请人： GENOMSYS SA
发明人： ALBERTI CLAUDIO , BALUCH MOHAMED KHOSO
IPC分类号： G16B45/00
摘要： The method and apparatus described in this disclosure include representing a reference genome in terms of syntax elements describing the differences between said reference genome and previously aligned genomic sequences. Each of the aligned genomic sequence is described by means of a subset of syntax elements. Syntax elements describing all the genomic sequences are partitioned in blocks according to their statistical properties. Each block of syntax elements is entropy coded. The entropy coded blocks are then concatenated to form a compressed bitstream. The differences between the reference genome and the aligned sequences are expressed in terms of syntax elements, which are embedded in the bitstream of coded blocks of syntax elements describing aligned reads. The disclosed method enables the reconstruction of the reference genome used for alignment when decoding the compressed genomic sequences while preserving different options of random access on the compressed data and enabling efficient compression.

7. 发明专利

PH12019550057A1 METHOD AND SYSTEMS FOR THE REPRESENTATION AND PROCESSING OF BIOINFORMATICS DATA USING REFERENCE SEQUENCES 未知
公开(公告)号：PH12019550057A1
公开(公告)日：2020-01-20
申请号：PH12019550057
申请日：2019-04-11
申请人： GENOMSYS SA
发明人： ALBERTI CLAUDIO , ZOIA GIORGIO , RENZI DANIELE , BALUCH MOHAMED KHOSO
IPC分类号： G16B45/00
摘要： Method and apparatus for the representation and processing of genome sequence data, produced by genome sequencing machines, when aligned on one or more reference sequences. Sequence reads are coded by aligning them with respect to pre-existing or constructed reference sequences. After the alignment, the coding process is composed of a classification of the reads into data classes, followed by the coding of each data class in terms of a multiplicity of descriptors layers. Specific source models and entropy coders are used for the coding of the sub-sets of descriptors used to represent each data class.

8. 发明专利

CL2019002276A1 Método y sistemas para la compresión eficiente de lecturas de secuencias genómicas. 未知
公开(公告)号：CL2019002276A1
公开(公告)日：2019-11-29
申请号：CL2019002276
申请日：2019-08-12
申请人： GENOMSYS SA
发明人： ALBERTI CLAUDIO , BALUCH MOHAMED KHOSO
IPC分类号： G16B45/00
摘要： MÉTODO Y APARATO PARA LA COMPRESIÓN DE DATOS DE SECUENCIAS DE GENOMAS PRODUCIDOS POR MÁQUINAS DE SECUENCIACIÓN DEL GENOMA. LAS LECTURAS DE SECUENCIAS SE CODIFICAN MEDIANTE SU ALINEACIÓN CON RESPECTO A SECUENCIAS DE REFERENCIA PREEXISTENTES O CONSTRUIDAS, EN DONDE EL PROCESO DE CODIFICACIÓN ESTÁ COMPUESTO POR UNA CLASIFICACIÓN DE LAS LECTURAS EN CLASES DE DATOS, A LO CUAL SIGUE LA CODIFICACIÓN DE CADA CLASE EN TÉRMINOS DE UNA MULTIPLICIDAD DE DESCRIPTORES GENÓMICOS. LOS DESCRIPTORES GENÓMICOS DEL MISMO TIPO SE ORGANIZAN EN BLOQUES QUE SE COMPRIMEN MEDIANTE LA APLICACIÓN DE SUCESIVAS ETAPAS DE TRANSFORMACIÓN, BINARIZACIÓN Y CODIFICACIÓN DE ENTROPÍA. SE UTILIZAN MODELOS DE FUENTE Y CODIFICADORES DE ENTROPÍA ESPECÍFICOS PARA CADA CLASE DE DATOS Y PARA CADA DESCRIPTOR ASOCIADO.

9. 发明专利

SG11201907417WA METHOD AND SYSTEMS FOR THE EFFICIENT COMPRESSION OF GENOMIC SEQUENCE READS 未知
公开(公告)号：SG11201907417WA
公开(公告)日：2019-09-27
申请号：SG11201907417W
申请日：2017-12-15
申请人： GENOMSYS SA
发明人： ALBERTI CLAUDIO , BALUCH MOHAMED KHOSO
摘要： rodIng rarrcters 1312 1304 305 1 bete once based alagoress4 f. \"2 , 11 (descr;pcors1 generator. C '77 3 , igr , ,mnts 1311 (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 23 August 2018 (23.08.2018) WIP0 I PCT O V SID o OH Em VIII VII IE (10) International Publication Number WO 2018/151788 Al (51) International Patent Classification: C4OB 50/02 (2006.01) GOOF 19/22 (2011.01) GOOF 19/26 (2011.01) (21) International Application Number: PCT/US2017/066863 (22) International Filing Date: 15 December 2017 (15.12.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: PCT/US2017/017842 14 February 2017 (14.02.2017) US PCT/US2017/041579 11 July 2017 (11.07.2017) US (71) Applicant: GENOMSYS SA [CH/CH]; Chemin de la Raye 13, 1024 Ecublens VD (CH). (72) Inventor; and (71) Applicant: BLAUCH, Mohamed, Khoso [US/US]; 4439 Woodsedge Ct, Chantilly, VA 20151 (US). (72) Inventor: ALBERTI, Claudio; Chemin des Esserts 1, 1213 Petit-Laney (Geneva) (CH). (74) Agent: BILICKI, Byron et al.; 1285 North Main St, Jamestown, NY 14750 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (54) Title: METHOD AND SYSTEMS FOR THE EFFICIENT COMPRESSION OF GENOMIC SEQUENCE READS 1309 a ding parameter.e.ncotie, Boad.tion Rinnnzation Binanzation —` ti `AI >inorintion ender Binallzatiop Entropy coder Binatt,ation —' Entropy Binaribdio ntrnp coder Entropy coder 1307 I nd Figure 13. (57) : Method and apparatus for the compression of genome sequence data produced by genome sequencing machines. Se- quence reads are coded by aligning them with respect to pre-existing or constructed reference sequences, the coding process is composed of a classification of the reads into data classes followed by the coding of each class in terms of a multiplicity of genomic descriptors. Genomic descriptors of the same type are organized in blocks which are compressed by applying successive transformation stages, bi- narization and entropy coding. Specific source models and entropy coders are used for each data class and for each associated descriptor. [Continued on next page] WO 2018/151788 Al MIDEDIMOMMIDIREEM3111111111111111111111101111111111111111111 (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Published: with international search report (Art. 21(3)) before the expiration of the time limit for amending the claims and to be republished in the event of receipt of amendments (Rule 48.2(h))

10. 发明专利

CL2019000968A1 Método y sistema para el acceso selectivo de datos bioinformáticos almacenados o transmitidos. 未知
公开(公告)号：CL2019000968A1
公开(公告)日：2019-08-23
申请号：CL2019000968
申请日：2019-04-10
申请人： GENOMSYS SA
发明人： RENZI DANIELE , ZOIA GIORGIO , BALUCH MOHAMED KHOSO
IPC分类号： G16B45/00
摘要： EL ALMACENAMIENTO O LA TRANSMISIÓN DE DATOS GENÓMICOS SE REALIZA EMPLEANDO UN CONJUNTO DE DATOS GENÓMICOS COMPRIMIDOS ESTRUCTURADOS EN UN ARCHIVO O EN UN FLUJO DE DATOS GENÓMICOS. EL ACCESO SELECTIVO A LOS DATOS, O SUBCONJUNTOS DE LOS DATOS, CORRESPONDIENTES A REGIONES GENÓMICAS ESPECÍFICAS SE LOGRA AL EMPLEAR ETIQUETAS DEFINIDAS POR EL USUARIO BASADAS EN LA CLASIFICACIÓN DE DATOS Y UN MECANISMO DE INDEXACIÓN ESPECÍFICO.

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