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Without detailed genomic\/gene information, <jats:italic>in silico<\/jats:italic> sequence determination is not straightforward, and full coding sequence determination typically involves time- and labor-intensive PCR-based amplification and cloning methods.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>An improved method was developed with which to determine full length gene coding sequences <jats:italic>in silico<\/jats:italic> using <jats:italic>de novo<\/jats:italic> assembly of RNA-Seq data. The scheme improves upon initial contigs through contig-to-gene identification by BLAST nearest\u2013neighbor comparison, and through single-contig refinement by iterative-binning and -assembly of reads. Application of the iterative method produced the gene identification and full coding sequence for 9 of 12 genes and improved the sequence of 3 of the 12 genes targeted by benzimidazole, macrocyclic lactone, and nicotinic agonist classes of anthelminthic drugs in the swine nodular parasite <jats:italic>Oesophagostomum dentatum<\/jats:italic>. The approach improved upon the initial optimized assembly with Velvet that only identified full coding sequences for 2 genes.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Our reiterative methodology represents a simplified pipeline with which to determine longer gene sequences <jats:italic>in silico<\/jats:italic> from next generation sequence data for any nematode for which detailed genetic\/gene information is lacking. The method significantly improved upon an initial Velvet assembly of RNA-Seq data that yielded only 2 full length sequences. The identified coding sequences for the 11 target genes enables further future examinations including: (i) the use of recombinant target protein in functional assays seeking a better understanding of the mechanism of drug resistance, and (ii) seeking comparative genomic and transcriptomic assessments between parasite isolates that exhibit varied drug sensitivities.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2156-14-55","type":"journal-article","created":{"date-parts":[[2013,6,18]],"date-time":"2013-06-18T08:14:38Z","timestamp":1371543278000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Computational cloning of drug target genes of a parasitic nematode, Oesophagostomum dentatum"],"prefix":"10.1186","volume":"14","author":[{"given":"Nathan M","family":"Romine","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard J","family":"Martin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey K","family":"Beetham","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,6,18]]},"reference":[{"issue":"10","key":"1121_CR1","doi-asserted-by":"publisher","first-page":"1137","DOI":"10.1016\/j.ijpara.2010.04.004","volume":"40","author":"S Brooker","year":"2010","unstructured":"Brooker S: Estimating the global distribution and disease burden of intestinal nematode infections: adding up the numbers\u2013a review. 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