{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T05:26:41Z","timestamp":1674624401033},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output.<\/jats:p>\n               <jats:p>Availability: . GenoMiner software and documentation is available from the authors upon request.<\/jats:p>\n               <jats:p>Contact: \u00a0graziano.pesole@unimi.it<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti754","type":"journal-article","created":{"date-parts":[[2005,11,3]],"date-time":"2005-11-03T01:13:48Z","timestamp":1130980428000},"page":"497-499","source":"Crossref","is-referenced-by-count":4,"title":["GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags"],"prefix":"10.1093","volume":"22","author":[{"given":"Tiziana","family":"Castrignan\u00f2","sequence":"first","affiliation":[{"name":"Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universit\u00e0e Ricerca, CASPUR 1 \u00a0 1 \u00a0 \u00a0 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paolo D'Onorio","family":"De Meo","sequence":"additional","affiliation":[{"name":"Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universit\u00e0e Ricerca, CASPUR 1 \u00a0 1 \u00a0 \u00a0 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giorgio","family":"Grillo","sequence":"additional","affiliation":[{"name":"Istituto Tecnologie Biomediche, Sede di Bari 2 \u00a0 2 \u00a0 \u00a0 Consiglio Nazionale delle Ricerche, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabino","family":"Liuni","sequence":"additional","affiliation":[{"name":"Istituto Tecnologie Biomediche, Sede di Bari 2 \u00a0 2 \u00a0 \u00a0 Consiglio Nazionale delle Ricerche, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Flavio","family":"Mignone","sequence":"additional","affiliation":[{"name":"University of Milan, Dipartimento di Scienze Biomolecolari e Biotecnologie 3 \u00a0 3 \u00a0 \u00a0 via Celoria 26, Milan 20133, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivano Giuseppe","family":"Talamo","sequence":"additional","affiliation":[{"name":"Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Universit\u00e0e Ricerca, CASPUR 1 \u00a0 1 \u00a0 \u00a0 Rome, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Graziano","family":"Pesole","sequence":"additional","affiliation":[{"name":"Istituto Tecnologie Biomediche, Sede di Bari 2 \u00a0 2 \u00a0 \u00a0 Consiglio Nazionale delle Ricerche, Italy"},{"name":"University of Milan, Dipartimento di Scienze Biomolecolari e Biotecnologie 3 \u00a0 3 \u00a0 \u00a0 via Celoria 26, Milan 20133, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2005,11,2]]},"reference":[{"issue":"Web Server issue","key":"2023012408502061600_b1","doi-asserted-by":"crossref","first-page":"W624","DOI":"10.1093\/nar\/gkh486","article-title":"CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison","volume":"32","author":"Castrignano","year":"2004","journal-title":"Nucleic Acids Res."},{"issue":"Database issue","key":"2023012408502061600_b2","doi-asserted-by":"crossref","first-page":"D447","DOI":"10.1093\/nar\/gki138","article-title":"Ensembl 2005","volume":"33","author":"Hubbard","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012408502061600_b3","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1093\/nar\/gkg129","article-title":"The UCSC Genome Browser Database","volume":"31","author":"Karolchik","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012408502061600_b4","first-page":"656","article-title":"BLAT\u2014the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023012408502061600_b5","doi-asserted-by":"crossref","first-page":"4639","DOI":"10.1093\/nar\/gkg483","article-title":"Computational identification of protein coding potential of conserved sequence tags through cross-species evolutionary analysis","volume":"31","author":"Mignone","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012408502061600_b6","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1146\/annurev.genom.5.061903.180057","article-title":"Comparative genomics","volume":"5","author":"Miller","year":"2004","journal-title":"Annu. 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