{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T02:22:16Z","timestamp":1775787736958,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2021,2,12]],"date-time":"2021-02-12T00:00:00Z","timestamp":1613088000000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IOS 1546858"],"award-info":[{"award-number":["IOS 1546858"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["ACI-1548562"],"award-info":[{"award-number":["ACI-1548562"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["TG-MCB190098"],"award-info":[{"award-number":["TG-MCB190098"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["TG-MCB200123"],"award-info":[{"award-number":["TG-MCB200123"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"XSEDE"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Searching for open reading frames is a routine task and a critical step prior to annotating protein coding regions in newly sequenced genomes or de novo transcriptome assemblies. With the tremendous increase in genomic and transcriptomic data, faster tools are needed to handle large input datasets. These tools should be versatile enough to fine-tune search criteria and allow efficient downstream analysis. Here we present a new python based tool, orfipy, which allows the user to flexibly search for open reading frames in genomic and transcriptomic sequences. The search is rapid and is fully customizable, with a choice of FASTA and BED output formats.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>orfipy is implemented in python and is compatible with python v3.6 and higher. Source code: https:\/\/github.com\/urmi-21\/orfipy. Installation: from the source, or via PyPi (https:\/\/pypi.org\/project\/orfipy) or bioconda (https:\/\/anaconda.org\/bioconda\/orfipy).<\/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\/btab090","type":"journal-article","created":{"date-parts":[[2021,2,4]],"date-time":"2021-02-04T01:07:18Z","timestamp":1612400838000},"page":"3019-3020","source":"Crossref","is-referenced-by-count":93,"title":["orfipy: a fast and flexible tool for extracting ORFs"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3703-0820","authenticated-orcid":false,"given":"Urminder","family":"Singh","sequence":"first","affiliation":[{"name":"Bioinformatics and Computational Biology Program, Iowa State University, Ames , IA 50011, USA"},{"name":"Center for Metabolic Biology, Iowa State University , Ames, IA 50011, USA"},{"name":"Department of Genetics Development and Cell Biology, Iowa State University, Ames , IA 50011, USA"}]},{"given":"Eve Syrkin","family":"Wurtele","sequence":"additional","affiliation":[{"name":"Bioinformatics and Computational Biology Program, Iowa State University, Ames , IA 50011, USA"},{"name":"Center for Metabolic Biology, Iowa State University , Ames, IA 50011, USA"},{"name":"Department of Genetics Development and Cell Biology, Iowa State University, Ames , IA 50011, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,2,8]]},"reference":[{"key":"2023061310472219400_btab090-B1","article-title":"Pyfastx: a robust python package for fast random access to sequences from plain and gzipped fasta\/q files","author":"Du","year":"2020","journal-title":"Brief. 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