{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:09Z","timestamp":1740185109163,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,10,18]],"date-time":"2020-10-18T00:00:00Z","timestamp":1602979200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Marie Sklodowska-Curie","award":["642095"],"award-info":[{"award-number":["642095"]}]},{"name":"Industrial Doctorates of MINECO","award":["DI-17-09134"],"award-info":[{"award-number":["DI-17-09134"]}]},{"name":"Digital Advancement of Ministry of Economic Affairs and Digital Transformation","award":["TSI-100903-2019-11"],"award-info":[{"award-number":["TSI-100903-2019-11"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA\/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user\u2019s expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences\u2019 analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Result<\/jats:title>\n                  <jats:p>SeqEditor is a cross-platform desktop application for the analysis of nucleotide and protein sequences. It is managed through a Graphical User Interface and can work either as a graphical sequence browser or as a fasta task manager for multi-fasta files. SeqEditor has been optimized for the management of large sequences, such as contigs, scaffolds or even chromosomes, and includes a GTF\/GFF viewer to visualize and manage annotation files. In turn, this allows for content mining from reference genomes and transcriptomes with similar efficiency to that of command line tools. SeqEditor also incorporates a set of tools for singleplex and multiplex PCR primer design and pooling that uses a newly optimized and validated search strategy for target and species-specific primers. All these features make SeqEditor a flexible application that can be used to analyses complex sequences, design primers in PCR assays oriented for diagnosis, and\/or manage, edit and personalize reference sequence datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>SeqEditor was developed in Java using Eclipse Rich Client Platform and is publicly available at https:\/\/gpro.biotechvana.com\/download\/SeqEditor as binaries for Windows, Linux and Mac OS. The user manual and tutorials are available online at https:\/\/gpro.biotechvana.com\/tool\/seqeditor\/manual.<\/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\/btaa903","type":"journal-article","created":{"date-parts":[[2020,10,7]],"date-time":"2020-10-07T12:02:40Z","timestamp":1602072160000},"page":"1610-1612","source":"Crossref","is-referenced-by-count":6,"title":["SeqEditor: an application for primer design and sequence analysis with or without GTF\/GFF files"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2343-5029","authenticated-orcid":false,"given":"Ahmed","family":"Hafez","sequence":"first","affiliation":[{"name":"Biotechvana, Parc Cient\u00edfic Universitat de Val\u00e8ncia , Valencia, Spain"},{"name":"Department of Experimental and Health Sciences, Universitat Pompeu Fabra , Barcelona, Spain"},{"name":"Faculty of Computers and Information, Minia University , Minia, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ricardo","family":"Futami","sequence":"additional","affiliation":[{"name":"Biotechvana, Parc Cient\u00edfic Universitat de Val\u00e8ncia , Valencia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amir","family":"Arastehfar","sequence":"additional","affiliation":[{"name":"Hackensack Meridian Health Center for Discovery and Innovation , Nutley, NJ 07110, USA"},{"name":"Westerdijk Fungal Biodiversity Institute , Utrecht, The Netherlands"},{"name":"Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam , Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Farnaz","family":"Daneshnia","sequence":"additional","affiliation":[{"name":"Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam , Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana","family":"Miguel","sequence":"additional","affiliation":[{"name":"Biotechvana, Parc Cient\u00edfic Universitat de Val\u00e8ncia , Valencia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Francisco J.","family":"Roig","sequence":"additional","affiliation":[{"name":"Biotechvana, Parc Cient\u00edfic Universitat de Val\u00e8ncia , Valencia, Spain"},{"name":"Facultad de Ciencias de la Salud, Universidad San Jorge , Zaragoza, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beatriz","family":"Soriano","sequence":"additional","affiliation":[{"name":"Biotechvana, Parc Cient\u00edfic Universitat de Val\u00e8ncia , Valencia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaume","family":"Perez-S\u00e1nchez","sequence":"additional","affiliation":[{"name":"Institute of Aquaculture Torre de la Sal (CSIC) , Castell\u00f3n, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Teun","family":"Boekhout","sequence":"additional","affiliation":[{"name":"Westerdijk Fungal Biodiversity Institute , Utrecht, The Netherlands"},{"name":"Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam , Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Toni","family":"Gabald\u00f3n","sequence":"additional","affiliation":[{"name":"Department of Experimental and Health Sciences, Universitat Pompeu Fabra , Barcelona, Spain"},{"name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats , Barcelona, Spain"},{"name":"Barcelona Supercomputing Centre (BSC-CNS) , Barcelona, Spain"},{"name":"Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology , Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlos","family":"Llorens","sequence":"additional","affiliation":[{"name":"Biotechvana, Parc Cient\u00edfic Universitat de Val\u00e8ncia , Valencia, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,10,18]]},"reference":[{"key":"2023051709442302400_btaa903-B1","doi-asserted-by":"crossref","first-page":"90","DOI":"10.3390\/jof5040090","article-title":"Identification of mycoses in developing countries","volume":"5","author":"Arastehfar","year":"2019","journal-title":"J. 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