{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T08:01:10Z","timestamp":1773216070032,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,11,21]],"date-time":"2016-11-21T00:00:00Z","timestamp":1479686400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"name":"Leloir Institute foundation and PICT","award":["2014-1787"],"award-info":[{"award-number":["2014-1787"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>MIToS is an environment for mutual information analysis and a framework for protein multiple sequence alignments (MSAs) and protein structures (PDB) management in Julia language. It integrates sequence and structural information through SIFTS, making Pfam MSAs analysis straightforward. MIToS streamlines the implementation of any measure calculated from residue contingency tables and its optimization and testing in terms of protein contact prediction. As an example, we implemented and tested a BLOSUM62-based pseudo-count strategy in mutual information analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The software is totally implemented in Julia and supported for Linux, OS X and Windows. It\u2019s freely available on GitHub under MIT license: http:\/\/mitos.leloir.org.ar.<\/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\/btw646","type":"journal-article","created":{"date-parts":[[2016,10,13]],"date-time":"2016-10-13T19:06:07Z","timestamp":1476385567000},"page":"564-565","source":"Crossref","is-referenced-by-count":19,"title":["MIToS.jl: mutual information tools for protein sequence analysis in the Julia language"],"prefix":"10.1093","volume":"33","author":[{"given":"Diego J","family":"Zea","sequence":"first","affiliation":[{"name":"Structural Bioinformatics Unit, Fundaci\u00f3n Instituto Leloir, C1405BWE, Ciudad Aut\u00f3noma de Buenos Aires, Argentina"}]},{"given":"Diego","family":"Anfossi","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics Unit, Fundaci\u00f3n Instituto Leloir, C1405BWE, Ciudad Aut\u00f3noma de Buenos Aires, Argentina"}]},{"given":"Morten","family":"Nielsen","sequence":"additional","affiliation":[{"name":"Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark"},{"name":"Instituto de Investigaciones Biotecnol\u00f3gicas, Universidad Nacional de San Mart\u00edn, 1650 San Mart\u00edn, Buenos Aires, Argentina"}]},{"given":"Cristina","family":"Marino-Buslje","sequence":"additional","affiliation":[{"name":"Structural Bioinformatics Unit, Fundaci\u00f3n Instituto Leloir, C1405BWE, Ciudad Aut\u00f3noma de Buenos Aires, Argentina"}]}],"member":"286","published-online":{"date-parts":[[2016,11,21]]},"reference":[{"key":"2023020204422642100_btw646-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023020204422642100_btw646-B2","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1093\/bioinformatics\/btp135","article-title":"Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information","volume":"25","author":"Buslje","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020204422642100_btw646-B3","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/nrg3414","article-title":"Emerging methods in protein co-evolution","volume":"14","author":"de Juan","year":"2013","journal-title":"Nat. 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Biol"},{"key":"2023020204422642100_btw646-B8","doi-asserted-by":"crossref","first-page":"D483","DOI":"10.1093\/nar\/gks1258","article-title":"SIFTS: Structure Integration with Function, Taxonomy and Sequences resource","volume":"41","author":"Velankar","year":"2013","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/4\/564\/49037678\/bioinformatics_33_4_564.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/4\/564\/49037678\/bioinformatics_33_4_564.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:46:57Z","timestamp":1675313217000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/4\/564\/2608634"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2016,11,21]]},"references-count":8,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2017,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw646","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,2,15]]},"published":{"date-parts":[[2016,11,21]]}}}