{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T11:16:45Z","timestamp":1772191005657,"version":"3.50.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2021,5,10]],"date-time":"2021-05-10T00:00:00Z","timestamp":1620604800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/B\/000C0427"],"award-info":[{"award-number":["BBS\/E\/B\/000C0427"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BBS\/E\/B\/000C0428"],"award-info":[{"award-number":["BBS\/E\/B\/000C0428"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"name":"BBSRC CASE studentship","award":["BB\/L016745\/1"],"award-info":[{"award-number":["BB\/L016745\/1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,10,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The annotation of small open reading frames (smORFs) of &amp;lt;100 codons (&amp;lt;300 nucleotides) is challenging due to the large number of such sequences in the genome.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this study, we developed a computational pipeline, which we have named ORFLine, that stringently identifies smORFs and classifies them according to their position within transcripts. We identified a total of 5744 unique smORFs in datasets from mouse B and T lymphocytes and systematically characterized them using ORFLine. We further searched smORFs for the presence of a signal peptide, which predicted known secreted chemokines as well as novel micropeptides. Four novel micropeptides show evidence of secretion and are therefore candidate mediators of immunoregulatory functions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Freely available on the web at https:\/\/github.com\/boboppie\/ORFLine.<\/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\/btab339","type":"journal-article","created":{"date-parts":[[2021,4,30]],"date-time":"2021-04-30T15:18:09Z","timestamp":1619795889000},"page":"3152-3159","source":"Crossref","is-referenced-by-count":14,"title":["ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes"],"prefix":"10.1093","volume":"37","author":[{"given":"Fengyuan","family":"Hu","sequence":"first","affiliation":[{"name":"Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK"}]},{"given":"Jia","family":"Lu","sequence":"additional","affiliation":[{"name":"Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK"}]},{"given":"Louise S","family":"Matheson","sequence":"additional","affiliation":[{"name":"Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9227-7474","authenticated-orcid":false,"given":"Manuel D","family":"D\u00edaz-Mu\u00f1oz","sequence":"additional","affiliation":[{"name":"Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK"}]},{"given":"Alexander","family":"Saveliev","sequence":"additional","affiliation":[{"name":"Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK"}]},{"given":"Jinbo","family":"Xu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3801-9896","authenticated-orcid":false,"given":"Martin","family":"Turner","sequence":"additional","affiliation":[{"name":"Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus , Cambridge CB22 3AT, UK"}]}],"member":"286","published-online":{"date-parts":[[2021,5,10]]},"reference":[{"key":"2023051608275693700_btab339-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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