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Identification of Common Carp Innate Immune Genes with Whole-Genome Sequencing and RNA-Seq Data

Zhang, Yanju ; Stupka, Elia ; Henkel, Christiaan V. ; Jansen, Hans J. ; Spaink, Herman P. ; Verbeek, Fons J.

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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Abstract:
The common carp is a candidate model system for immunology research. Using next-generation sequencing technology, we have generated a huge amount of sequence reads from the carp genome and transcriptome. Currently, our aim is to identify carp genes involved in the development of the innate immune response, particularly TIR domain-containing genes, from a preliminary genome assembly. To achieve this, we developed a comprehensive gene identification pipeline. This analysis allowed us to estimate that the carp has 39 TIR domain-containing transcript isoforms and genes.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Zhang, Yanju ; Stupka, Elia ; Henkel, Christiaan V. ; Jansen, Hans J. ; Spaink, Herman P. ; Verbeek, Fons J.  (2011)  Identification of Common Carp Innate Immune Genes with Whole-Genome Sequencing and RNA-Seq Data. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 8(2), 2011

Online-Journal: http://journal.imbio.de/article.php?aid=169
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2011/5185



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