Syncmer-based evolutionary distance estimation and phylogenetic tree construction method

Syncmer-based evolutionary distance estimation and phylogenetic tree construction method

The invention discloses a syncmer-based evolutionary distance estimation and phylogenetic tree construction method. The method comprises the following steps of reading a sequence file and performing primary processing on a sequence; all kmer with the length of k on the sequence are traversed, and sm...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Hauptverfasser: WANG YAOBIN, NIE JINTONG, LIU HUAN, HUANG FAJUN, LUO MINZHONG
Format: Patent
Sprache:chi ; eng
Schlagworte:
INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS
PHYSICS
Online-Zugang:Volltext bestellen
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page
container_issue
container_start_page
container_title
container_volume
creator WANG YAOBIN
NIE JINTONG
LIU HUAN
HUANG FAJUN
LUO MINZHONG
description The invention discloses a syncmer-based evolutionary distance estimation and phylogenetic tree construction method. The method comprises the following steps of reading a sequence file and performing primary processing on a sequence; all kmer with the length of k on the sequence are traversed, and smer with the minimum hash value on the kmer is found and judged; according to a MinHash algorithm, n syncmers with minimum hash values are finally reserved to form a sketch; comparing the sketches in pairs to calculate an evolutionary distance matrix; and converting the distance matrix into a phylogenetic tree. The objective of the invention is to solve the problems that when a conventional phylogenetic tree construction method based on distance is used for processing a large-scale data set, resource consumption is increased, calculation efficiency is reduced, accuracy is reduced, expansibility is poor, and stability cannot be maintained when a sequence is subjected to local mutation. The invention provides the sync
format Patent
fullrecord <record><control><sourceid>epo_EVB</sourceid><recordid>TN_cdi_epo_espacenet_CN118824374A</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>CN118824374A</sourcerecordid><originalsourceid>FETCH-epo_espacenet_CN118824374A3</originalsourceid><addsrcrecordid>eNqNjLEKwjAURbM4iPoPzw_oUFuwqxTFyUUHt_JMrjaQJiV5FfL3UvEDnA4cDmep7tfs9YBYPDjBEN7BTWKD55jJ2CTsNQhJ7MCzJvaGxj678IKHWE0SAdLBJ4mT_iYDpA9mrRZPdgmbH1dqezre2nOBMXRII-t50LWXsmyaXV3t60P1T_MBTs87qw</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>patent</recordtype></control><display><type>patent</type><title>Syncmer-based evolutionary distance estimation and phylogenetic tree construction method</title><source>esp@cenet</source><creator>WANG YAOBIN ; NIE JINTONG ; LIU HUAN ; HUANG FAJUN ; LUO MINZHONG</creator><creatorcontrib>WANG YAOBIN ; NIE JINTONG ; LIU HUAN ; HUANG FAJUN ; LUO MINZHONG</creatorcontrib><description>The invention discloses a syncmer-based evolutionary distance estimation and phylogenetic tree construction method. The method comprises the following steps of reading a sequence file and performing primary processing on a sequence; all kmer with the length of k on the sequence are traversed, and smer with the minimum hash value on the kmer is found and judged; according to a MinHash algorithm, n syncmers with minimum hash values are finally reserved to form a sketch; comparing the sketches in pairs to calculate an evolutionary distance matrix; and converting the distance matrix into a phylogenetic tree. The objective of the invention is to solve the problems that when a conventional phylogenetic tree construction method based on distance is used for processing a large-scale data set, resource consumption is increased, calculation efficiency is reduced, accuracy is reduced, expansibility is poor, and stability cannot be maintained when a sequence is subjected to local mutation. The invention provides the sync</description><language>chi ; eng</language><subject>INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS ; PHYSICS</subject><creationdate>2024</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&amp;date=20241022&amp;DB=EPODOC&amp;CC=CN&amp;NR=118824374A$$EHTML$$P50$$Gepo$$Hfree_for_read</linktohtml><link.rule.ids>230,308,776,881,25542,76289</link.rule.ids><linktorsrc>$$Uhttps://worldwide.espacenet.com/publicationDetails/biblio?FT=D&amp;date=20241022&amp;DB=EPODOC&amp;CC=CN&amp;NR=118824374A$$EView_record_in_European_Patent_Office$$FView_record_in_$$GEuropean_Patent_Office$$Hfree_for_read</linktorsrc></links><search><creatorcontrib>WANG YAOBIN</creatorcontrib><creatorcontrib>NIE JINTONG</creatorcontrib><creatorcontrib>LIU HUAN</creatorcontrib><creatorcontrib>HUANG FAJUN</creatorcontrib><creatorcontrib>LUO MINZHONG</creatorcontrib><title>Syncmer-based evolutionary distance estimation and phylogenetic tree construction method</title><description>The invention discloses a syncmer-based evolutionary distance estimation and phylogenetic tree construction method. The method comprises the following steps of reading a sequence file and performing primary processing on a sequence; all kmer with the length of k on the sequence are traversed, and smer with the minimum hash value on the kmer is found and judged; according to a MinHash algorithm, n syncmers with minimum hash values are finally reserved to form a sketch; comparing the sketches in pairs to calculate an evolutionary distance matrix; and converting the distance matrix into a phylogenetic tree. The objective of the invention is to solve the problems that when a conventional phylogenetic tree construction method based on distance is used for processing a large-scale data set, resource consumption is increased, calculation efficiency is reduced, accuracy is reduced, expansibility is poor, and stability cannot be maintained when a sequence is subjected to local mutation. The invention provides the sync</description><subject>INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS</subject><subject>PHYSICS</subject><fulltext>true</fulltext><rsrctype>patent</rsrctype><creationdate>2024</creationdate><recordtype>patent</recordtype><sourceid>EVB</sourceid><recordid>eNqNjLEKwjAURbM4iPoPzw_oUFuwqxTFyUUHt_JMrjaQJiV5FfL3UvEDnA4cDmep7tfs9YBYPDjBEN7BTWKD55jJ2CTsNQhJ7MCzJvaGxj678IKHWE0SAdLBJ4mT_iYDpA9mrRZPdgmbH1dqezre2nOBMXRII-t50LWXsmyaXV3t60P1T_MBTs87qw</recordid><startdate>20241022</startdate><enddate>20241022</enddate><creator>WANG YAOBIN</creator><creator>NIE JINTONG</creator><creator>LIU HUAN</creator><creator>HUANG FAJUN</creator><creator>LUO MINZHONG</creator><scope>EVB</scope></search><sort><creationdate>20241022</creationdate><title>Syncmer-based evolutionary distance estimation and phylogenetic tree construction method</title><author>WANG YAOBIN ; NIE JINTONG ; LIU HUAN ; HUANG FAJUN ; LUO MINZHONG</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-epo_espacenet_CN118824374A3</frbrgroupid><rsrctype>patents</rsrctype><prefilter>patents</prefilter><language>chi ; eng</language><creationdate>2024</creationdate><topic>INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS</topic><topic>PHYSICS</topic><toplevel>online_resources</toplevel><creatorcontrib>WANG YAOBIN</creatorcontrib><creatorcontrib>NIE JINTONG</creatorcontrib><creatorcontrib>LIU HUAN</creatorcontrib><creatorcontrib>HUANG FAJUN</creatorcontrib><creatorcontrib>LUO MINZHONG</creatorcontrib><collection>esp@cenet</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>WANG YAOBIN</au><au>NIE JINTONG</au><au>LIU HUAN</au><au>HUANG FAJUN</au><au>LUO MINZHONG</au><format>patent</format><genre>patent</genre><ristype>GEN</ristype><title>Syncmer-based evolutionary distance estimation and phylogenetic tree construction method</title><date>2024-10-22</date><risdate>2024</risdate><abstract>The invention discloses a syncmer-based evolutionary distance estimation and phylogenetic tree construction method. The method comprises the following steps of reading a sequence file and performing primary processing on a sequence; all kmer with the length of k on the sequence are traversed, and smer with the minimum hash value on the kmer is found and judged; according to a MinHash algorithm, n syncmers with minimum hash values are finally reserved to form a sketch; comparing the sketches in pairs to calculate an evolutionary distance matrix; and converting the distance matrix into a phylogenetic tree. The objective of the invention is to solve the problems that when a conventional phylogenetic tree construction method based on distance is used for processing a large-scale data set, resource consumption is increased, calculation efficiency is reduced, accuracy is reduced, expansibility is poor, and stability cannot be maintained when a sequence is subjected to local mutation. The invention provides the sync</abstract><oa>free_for_read</oa></addata></record>
fulltext fulltext_linktorsrc
identifier
ispartof
issn
language chi ; eng
recordid cdi_epo_espacenet_CN118824374A
source esp@cenet
subjects INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS
PHYSICS
title Syncmer-based evolutionary distance estimation and phylogenetic tree construction method
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-07T18%3A00%3A46IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-epo_EVB&rft_val_fmt=info:ofi/fmt:kev:mtx:patent&rft.genre=patent&rft.au=WANG%20YAOBIN&rft.date=2024-10-22&rft_id=info:doi/&rft_dat=%3Cepo_EVB%3ECN118824374A%3C/epo_EVB%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_id=info:pmid/&rfr_iscdi=true