{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,7,4]],"date-time":"2023-07-04T04:23:22Z","timestamp":1688444602999},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Cancer researchers seeking immunotherapy targets in cancer cells need tools to locate highly expressed proteins unique to cancer cells. Missense mutation and frameshift location reporter (MMuFLR), a Galaxy-based workflow, analyzes next-generation sequencing paired read RNA-seq output to reliably identify small frameshift mutations and missense mutations in highly expressed protein-coding genes. MMuFLR ignores known SNPs, low quality reads and poly-A\/T sequences. For each frameshift and missense mutation identified, MMuFLR provides the location and sequence of the amino acid substitutions in the novel protein candidates for direct input into epitope evaluation tools.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/toolshed.g2.bx.psu.edu\/<\/jats:p>\n               <jats:p>Contact: \u00a0rath0096@umn.edu or johns198@umn.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt385","type":"journal-article","created":{"date-parts":[[2013,7,4]],"date-time":"2013-07-04T07:00:34Z","timestamp":1372921234000},"page":"2353-2354","source":"Crossref","is-referenced-by-count":2,"title":["MMuFLR: missense mutation and frameshift location reporter"],"prefix":"10.1093","volume":"29","author":[{"given":"Susan K.","family":"Rathe","sequence":"first","affiliation":[{"name":"1 Masonic Cancer Center, 2Supercomputing Institute for Advanced Computation Research, 3Department of Genetics, Cell Biology and Development, 4Brain Tumor Program and 5Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA"}]},{"given":"James E.","family":"Johnson","sequence":"additional","affiliation":[{"name":"1 Masonic Cancer Center, 2Supercomputing Institute for Advanced Computation Research, 3Department of Genetics, Cell Biology and Development, 4Brain Tumor Program and 5Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA"}]},{"given":"Kevin A.T.","family":"Silverstein","sequence":"additional","affiliation":[{"name":"1 Masonic Cancer Center, 2Supercomputing Institute for Advanced Computation Research, 3Department of Genetics, Cell Biology and Development, 4Brain Tumor Program and 5Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA"}]},{"given":"Jesse J.","family":"Erdmann","sequence":"additional","affiliation":[{"name":"1 Masonic Cancer Center, 2Supercomputing Institute for Advanced Computation Research, 3Department of Genetics, Cell Biology and Development, 4Brain Tumor Program and 5Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA"}]},{"given":"Adrienne L.","family":"Watson","sequence":"additional","affiliation":[{"name":"1 Masonic Cancer Center, 2Supercomputing Institute for Advanced Computation Research, 3Department of Genetics, Cell Biology and Development, 4Brain Tumor Program and 5Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA"},{"name":"1 Masonic Cancer Center, 2Supercomputing Institute for Advanced Computation Research, 3Department of Genetics, Cell Biology and Development, 4Brain Tumor Program and 5Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA"},{"name":"1 Masonic Cancer Center, 2Supercomputing Institute for Advanced Computation Research, 3Department of Genetics, Cell Biology and Development, 4Brain Tumor Program and 5Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA"}]},{"given":"Flavia E.","family":"Popescu","sequence":"additional","affiliation":[{"name":"1 Masonic Cancer Center, 2Supercomputing Institute for Advanced Computation Research, 3Department of Genetics, Cell Biology and Development, 4Brain Tumor Program and 5Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA"}]},{"given":"John R.","family":"Ohlfest","sequence":"additional","affiliation":[{"name":"1 Masonic Cancer Center, 2Supercomputing Institute for Advanced Computation Research, 3Department of Genetics, Cell Biology and Development, 4Brain Tumor Program and 5Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA"}]},{"given":"David A.","family":"Largaespada","sequence":"additional","affiliation":[{"name":"1 Masonic Cancer Center, 2Supercomputing Institute for Advanced Computation Research, 3Department of Genetics, Cell Biology and Development, 4Brain Tumor Program and 5Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA"},{"name":"1 Masonic Cancer Center, 2Supercomputing Institute for Advanced Computation Research, 3Department of Genetics, Cell Biology and Development, 4Brain Tumor Program and 5Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA"},{"name":"1 Masonic Cancer Center, 2Supercomputing Institute for Advanced Computation Research, 3Department of Genetics, Cell Biology and Development, 4Brain Tumor Program and 5Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA"}]}],"member":"286","published-online":{"date-parts":[[2013,7,3]]},"reference":[{"key":"2023070311400504900_btt385-B1","doi-asserted-by":"crossref","DOI":"10.1002\/0471142727.mb1910s89","article-title":"Galaxy: a web-based genome analysis tool for experimentalists","author":"Blankenberg","year":"2010","journal-title":"Curr. 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