{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:04Z","timestamp":1772138044906,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2021,4,13]],"date-time":"2021-04-13T00:00:00Z","timestamp":1618272000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Transformation Science and Technology Program","award":["2018ZX08020002-005-003"],"award-info":[{"award-number":["2018ZX08020002-005-003"]}]},{"name":"Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding","award":["2016C02056-1"],"award-info":[{"award-number":["2016C02056-1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,10,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Sequence Processing and Data Extraction (SPDE) has eight modules comprising 100 basic functions ranging from sequence extraction, format conversion to data reorganization and mining, and all of these functions can be completed by point-and-click icons. SPDE also incorporates eight public analyses tools; thus, SPDE is a comprehensive bioinformatics platform for big biological data analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SPDE built by Python can run on 32-bit, 64-bit Windows and MacOS systems. It can be downloaded from https:\/\/github.com\/simon19891216\/SPDEv1.2.git.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab235","type":"journal-article","created":{"date-parts":[[2021,4,10]],"date-time":"2021-04-10T07:49:32Z","timestamp":1618040972000},"page":"3686-3687","source":"Crossref","is-referenced-by-count":30,"title":["SPDE: a multi-functional software for sequence processing and data extraction"],"prefix":"10.1093","volume":"37","author":[{"given":"Dong","family":"Xu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry , Beijing 100091, China"},{"name":"Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400, China"}]},{"given":"Zhuchou","family":"Lu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry , Beijing 100091, China"},{"name":"Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400, China"}]},{"given":"Kangming","family":"Jin","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry , Beijing 100091, China"},{"name":"Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400, China"}]},{"given":"Wenmin","family":"Qiu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry , Beijing 100091, China"},{"name":"Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400, China"}]},{"given":"Guirong","family":"Qiao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry , Beijing 100091, China"},{"name":"Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400, China"}]},{"given":"Xiaojiao","family":"Han","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry , Beijing 100091, China"},{"name":"Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400, China"}]},{"given":"Renying","family":"Zhuo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry , Beijing 100091, China"},{"name":"Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry , Hangzhou 311400, China"}]}],"member":"286","published-online":{"date-parts":[[2021,4,13]]},"reference":[{"key":"2023051608570996800_btab235-B1","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023051608570996800_btab235-B2","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. 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