Phylogenetic inference carried out concurrently with a sequencing operation
AssigneeInternational Business Machines Corporation
InventorsRITESH VIJAY KRISHNA, LAURA-JAYNE GARDINER, VADIM ELISSEEV
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Abstract
A method, computer program product, and computer system infer phylogenic relationships concurrently with a sequencing operation. The inferring includes, while sequencing data is in production by a sequencing machine, accessing the sequencing data, mapping sequence reads from the accessed sequencing data to identify sequence reads corresponding to orthologous genes of interest, and placing the identified sequence reads into respective namespaces for the corresponding orthologous genes in the in-memory database.
Claims20
A computer-implemented method for generating phylogenetic inferences using a distributed computing environment with an in-memory database, the computer-implemented method comprising:
- inferring phylogenetic relationships concurrently with a sequencing operation, wherein the inferring comprises, while sequencing data is in production by a sequencing machine:
- accessing the sequencing data;
- mapping sequence reads from the accessed sequencing data to identify sequence reads corresponding to orthologous genes of interest;
- and
- placing the identified sequence reads into respective namespaces for the corresponding orthologous genes in the in-memory database.
A system for generating phylogenetic inferences using a distributed computing environment with an in-memory database, comprising:
- a processor set;
- one or more computer-readable storage media;
- and
- program instructions stored on the one or more computer-readable storage media to cause the processor set to perform operations comprising:
- inferring phylogenetic relationships concurrently with a sequencing operation, wherein the inferring comprises, while sequencing data is in production by a sequencing machine:
- accessing the sequencing data;
- mapping sequence reads from the accessed sequencing data to identify sequence reads corresponding to orthologous genes of interest;
- and
- placing the identified sequence reads into respective namespaces for the corresponding orthologous genes in the in-memory database.
A computer program product for generating phylogenetic inferences using a distributed computing environment with an in-memory database, comprising:
- one or more computer-readable storage media;
- and
- program instructions stored on the one or more computer-readable storage media to perform operations comprising:
- inferring phylogenetic relationships concurrently with a sequencing operation, wherein the inferring comprises, while sequencing data is in production by a sequencing machine:
- accessing the sequencing data;
- mapping sequence reads from the accessed sequencing data to identify sequence reads corresponding to orthologous genes of interest;
- and
- placing the identified sequence reads into respective namespaces for the corresponding orthologous genes in the in-memory database.
Dependencies are inferred from the claim text.