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Integrated Modeling of Structural Genes Using MCuNovo

  • Xiaolong Cao
  • Haobo JiangEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1858)

Abstract

Correct modeling of protein-coding genes based on genome and cDNA data is a prerequisite for functional studies. Various programs such as MAKER, Cufflinks, Oases, and Trinity have been developed, each with advantages and drawbacks. Manual integration of different models for a single gene is cumbersome and becomes a daunting task for 14,000–18,000 genes in a typical holometabolous insect. We developed methods to evaluate the output of MAKER, Cufflinks, Oases and Trinity and select the best models to constitute the MCOT1.0 set for Manduca sexta, a biochemical model insect. To apply these methods in other organisms, we improved the algorithm (designated MCuNovo Gene Selector) and automated the data processing. In this chapter, we describe background information of algorithm development and how to prepare and run this program.

Key words

Insect Genomics Transcriptome Gene modeling Python Arthropod 

Notes

Acknowledgments

This study is supported by NIH grants GM58634 and AI112662. This work was approved for publication by the Director of Oklahoma Agricultural Experimental Station and supported in part under project OKLO2450.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Entomology and Plant PathologyOklahoma State UniversityStillwaterUSA

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