{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T03:07:48Z","timestamp":1774494468565,"version":"3.50.1"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2018,5,29]],"date-time":"2018-05-29T00:00:00Z","timestamp":1527552000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000069","name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","doi-asserted-by":"publisher","award":["P30-AR048335"],"award-info":[{"award-number":["P30-AR048335"]}],"id":[{"id":"10.13039\/100000069","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Many genomic features are defined not by exact sequence matches, but by degenerate nucleotide motifs that represent multiple compatible matches. While there are databases cataloging genomic features, such as the location of transcription factor motifs, for commonly used model species, identifying the locations of novel motifs, known motifs in non-model genomes, or known motifs in personal whole-genomes is difficult. I designed motif scraper to overcome this limitation, allowing for efficient, multiprocessor motif searches in any FASTA file.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The motif scraper package (MIT license) is available via PyPI, and the Python source is available on GitHub at https:\/\/github.com\/RobersonLab\/motif_scraper.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty437","type":"journal-article","created":{"date-parts":[[2018,5,23]],"date-time":"2018-05-23T15:16:35Z","timestamp":1527088595000},"page":"3926-3928","source":"Crossref","is-referenced-by-count":10,"title":["Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5921-2399","authenticated-orcid":false,"given":"Elisha D O","family":"Roberson","sequence":"first","affiliation":[{"name":"Department of Medicine, Division of Rheumatology, Washington University, St. Louis, MO, USA"},{"name":"Department of Genetics, Division of Rheumatology, Washington University, St. Louis, MO, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,5,29]]},"reference":[{"key":"2023012712370258800_bty437-B1","doi-asserted-by":"crossref","first-page":"e05005","DOI":"10.7554\/eLife.05005","article-title":"Predicting effective microRNA target sites in mammalian mRNAs","volume":"4","author":"Agarwal","year":"2015","journal-title":"Elife"},{"key":"2023012712370258800_bty437-B2","doi-asserted-by":"crossref","first-page":"bav035","DOI":"10.1093\/database\/bav035","article-title":"miRGate: a curated database of human, mouse and rat miRNA-mRNA targets","volume":"2015","author":"Andres-Leon","year":"2015","journal-title":"Database"},{"key":"2023012712370258800_bty437-B3","doi-asserted-by":"crossref","first-page":"W202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME SUITE: tools for motif discovery and searching","volume":"37","author":"Bailey","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023012712370258800_bty437-B4","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1007\/978-1-4939-1062-5_25","volume-title":"RNA Mapping: Methods and Protocols","author":"Dweep","year":"2014"},{"key":"2023012712370258800_bty437-B5","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1534\/genetics.113.160713","article-title":"Highly specific and efficient CRISPR\/Cas9-catalyzed homology-directed repair in Drosophila","volume":"196","author":"Gratz","year":"2014","journal-title":"Genetics"},{"key":"2023012712370258800_bty437-B6","doi-asserted-by":"crossref","first-page":"D109","DOI":"10.1093\/nar\/gkh023","article-title":"The microRNA registry","volume":"32","author":"Griffiths-Jones","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023012712370258800_bty437-B7","doi-asserted-by":"crossref","first-page":"D140","DOI":"10.1093\/nar\/gkj112","article-title":"miRBase: microRNA sequences, targets and gene nomenclature","volume":"34","author":"Griffiths-Jones","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023012712370258800_bty437-B8","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gkm952","article-title":"miRBase: tools for microRNA genomics","volume":"36","author":"Griffiths-Jones","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2023012712370258800_bty437-B9","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1038\/nmeth.2812","article-title":"E-CRISP: fast CRISPR target site identification","volume":"11","author":"Heigwer","year":"2014","journal-title":"Nat Methods"},{"key":"2023012712370258800_bty437-B10","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol. 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