SYSTEM AND METHOD FOR SEQUENCE IDENTIFICATION IN REASSEMBLY VARIANT CALLING
In one embodiment, a method for identifying candidate sequences for genotyping a genomic sample comprises obtaining a plurality of sequence reads mapping to a genomic region of interest. The plurality of sequence reads are assembled into a directed acyclic graph (DAG) comprising a plurality of branc...
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| creator | Johnson, Ivan |
| description | In one embodiment, a method for identifying candidate sequences for genotyping a genomic sample comprises obtaining a plurality of sequence reads mapping to a genomic region of interest. The plurality of sequence reads are assembled into a directed acyclic graph (DAG) comprising a plurality of branch sites representing variation present in the set of sequence reads, each branch site comprising two or more branches. A path through the DAG comprises a set of successive branches over two or more branch sites and represents a possible candidate sequence of the genomic sample. One or more paths through the DAG are ranked by calculating scores for one or more branch sites, wherein the calculated score comprises a number of sequence reads that span multiple branch sites in a given path. At least one path is selected as a candidate sequence based at least in part on its rank. |
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The plurality of sequence reads are assembled into a directed acyclic graph (DAG) comprising a plurality of branch sites representing variation present in the set of sequence reads, each branch site comprising two or more branches. A path through the DAG comprises a set of successive branches over two or more branch sites and represents a possible candidate sequence of the genomic sample. One or more paths through the DAG are ranked by calculating scores for one or more branch sites, wherein the calculated score comprises a number of sequence reads that span multiple branch sites in a given path. At least one path is selected as a candidate sequence based at least in part on its rank.</description><language>eng</language><subject>BEER ; BIOCHEMISTRY ; CHEMISTRY ; COMPOSITIONS OR TEST PAPERS THEREFOR ; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES ; ENZYMOLOGY ; INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS ; MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS ; METALLURGY ; MICROBIOLOGY ; MUTATION OR GENETIC ENGINEERING ; PHYSICS ; PROCESSES OF PREPARING SUCH COMPOSITIONS ; SPIRITS ; VINEGAR ; WINE</subject><creationdate>2019</creationdate><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://worldwide.espacenet.com/publicationDetails/biblio?FT=D&date=20190829&DB=EPODOC&CC=US&NR=2019267110A1$$EHTML$$P50$$Gepo$$Hfree_for_read</linktohtml><link.rule.ids>230,308,777,882,25545,76296</link.rule.ids><linktorsrc>$$Uhttps://worldwide.espacenet.com/publicationDetails/biblio?FT=D&date=20190829&DB=EPODOC&CC=US&NR=2019267110A1$$EView_record_in_European_Patent_Office$$FView_record_in_$$GEuropean_Patent_Office$$Hfree_for_read</linktorsrc></links><search><creatorcontrib>Johnson, Ivan</creatorcontrib><title>SYSTEM AND METHOD FOR SEQUENCE IDENTIFICATION IN REASSEMBLY VARIANT CALLING</title><description>In one embodiment, a method for identifying candidate sequences for genotyping a genomic sample comprises obtaining a plurality of sequence reads mapping to a genomic region of interest. The plurality of sequence reads are assembled into a directed acyclic graph (DAG) comprising a plurality of branch sites representing variation present in the set of sequence reads, each branch site comprising two or more branches. A path through the DAG comprises a set of successive branches over two or more branch sites and represents a possible candidate sequence of the genomic sample. One or more paths through the DAG are ranked by calculating scores for one or more branch sites, wherein the calculated score comprises a number of sequence reads that span multiple branch sites in a given path. At least one path is selected as a candidate sequence based at least in part on its rank.</description><subject>BEER</subject><subject>BIOCHEMISTRY</subject><subject>CHEMISTRY</subject><subject>COMPOSITIONS OR TEST PAPERS THEREFOR</subject><subject>CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES</subject><subject>ENZYMOLOGY</subject><subject>INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS</subject><subject>MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS</subject><subject>METALLURGY</subject><subject>MICROBIOLOGY</subject><subject>MUTATION OR GENETIC ENGINEERING</subject><subject>PHYSICS</subject><subject>PROCESSES OF PREPARING SUCH COMPOSITIONS</subject><subject>SPIRITS</subject><subject>VINEGAR</subject><subject>WINE</subject><fulltext>true</fulltext><rsrctype>patent</rsrctype><creationdate>2019</creationdate><recordtype>patent</recordtype><sourceid>EVB</sourceid><recordid>eNqNyrEKwjAQANAsDqL-w4Gz0FRQOp7p1R4mF0xSoVMpEifRQv1_XPwAp7e8pbrEPiZygFKDo9T6GhofINK1IzEEXJMkbthgYi_AAoEwRnIn28MNA6MkMGgty3mtFo_xOefNz5XaNpRMu8vTe8jzNN7zK3-GLpaFrsrDUesC9f6_9QVIei6g</recordid><startdate>20190829</startdate><enddate>20190829</enddate><creator>Johnson, Ivan</creator><scope>EVB</scope></search><sort><creationdate>20190829</creationdate><title>SYSTEM AND METHOD FOR SEQUENCE IDENTIFICATION IN REASSEMBLY VARIANT CALLING</title><author>Johnson, Ivan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-epo_espacenet_US2019267110A13</frbrgroupid><rsrctype>patents</rsrctype><prefilter>patents</prefilter><language>eng</language><creationdate>2019</creationdate><topic>BEER</topic><topic>BIOCHEMISTRY</topic><topic>CHEMISTRY</topic><topic>COMPOSITIONS OR TEST PAPERS THEREFOR</topic><topic>CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES</topic><topic>ENZYMOLOGY</topic><topic>INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS</topic><topic>MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS</topic><topic>METALLURGY</topic><topic>MICROBIOLOGY</topic><topic>MUTATION OR GENETIC ENGINEERING</topic><topic>PHYSICS</topic><topic>PROCESSES OF PREPARING SUCH COMPOSITIONS</topic><topic>SPIRITS</topic><topic>VINEGAR</topic><topic>WINE</topic><toplevel>online_resources</toplevel><creatorcontrib>Johnson, Ivan</creatorcontrib><collection>esp@cenet</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Johnson, Ivan</au><format>patent</format><genre>patent</genre><ristype>GEN</ristype><title>SYSTEM AND METHOD FOR SEQUENCE IDENTIFICATION IN REASSEMBLY VARIANT CALLING</title><date>2019-08-29</date><risdate>2019</risdate><abstract>In one embodiment, a method for identifying candidate sequences for genotyping a genomic sample comprises obtaining a plurality of sequence reads mapping to a genomic region of interest. The plurality of sequence reads are assembled into a directed acyclic graph (DAG) comprising a plurality of branch sites representing variation present in the set of sequence reads, each branch site comprising two or more branches. A path through the DAG comprises a set of successive branches over two or more branch sites and represents a possible candidate sequence of the genomic sample. One or more paths through the DAG are ranked by calculating scores for one or more branch sites, wherein the calculated score comprises a number of sequence reads that span multiple branch sites in a given path. At least one path is selected as a candidate sequence based at least in part on its rank.</abstract><oa>free_for_read</oa></addata></record> |
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| subjects | BEER BIOCHEMISTRY CHEMISTRY COMPOSITIONS OR TEST PAPERS THEREFOR CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES ENZYMOLOGY INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS METALLURGY MICROBIOLOGY MUTATION OR GENETIC ENGINEERING PHYSICS PROCESSES OF PREPARING SUCH COMPOSITIONS SPIRITS VINEGAR WINE |
| title | SYSTEM AND METHOD FOR SEQUENCE IDENTIFICATION IN REASSEMBLY VARIANT CALLING |
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