Practical guide for fungal gene prediction from genome assembly and RNA-seq reads by FunGAP

Byoungnam Min, In-Geol Choi

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

FunGAP is a Python-wrapped fungal genome annotation pipeline running under the Linux/Unix operating system. The annotation procedure used in FunGAP requires two inputs, genome assembly and RNA-seq reads. FunGAP aims to predict the most feasible gene from all plausible gene models obtained from various gene prediction programs using multiple strategies such as ab initio, EST-, and/or homology-based methods. This guide covers how to run the FunGAP from the command line and use various options for practical gene prediction. Users can choose options for quality control of the input sequences, selecting model database, filtration of predicted gene models, and post-process such as checking genome completeness and transposable elements. Using FunGAP, the user will acquire a high-quality fungal gene prediction for post-genome sequencing analysis.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages53-64
Number of pages12
DOIs
Publication statusPublished - 2019 Jan 1

Publication series

NameMethods in Molecular Biology
Volume1962
ISSN (Print)1064-3745

Fingerprint

Fungal Genes
Genome
RNA
Genes
Fungal Genome
Boidae
DNA Transposable Elements
Expressed Sequence Tags
Running
Quality Control
Databases

Keywords

  • Evidence-based prediction
  • Fungal gene prediction
  • Fungal genome annotation pipeline
  • FunGAP
  • Genome annotation
  • Genome assembly
  • RNA-seq

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Min, B., & Choi, I-G. (2019). Practical guide for fungal gene prediction from genome assembly and RNA-seq reads by FunGAP. In Methods in Molecular Biology (pp. 53-64). (Methods in Molecular Biology; Vol. 1962). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9173-0_4

Practical guide for fungal gene prediction from genome assembly and RNA-seq reads by FunGAP. / Min, Byoungnam; Choi, In-Geol.

Methods in Molecular Biology. Humana Press Inc., 2019. p. 53-64 (Methods in Molecular Biology; Vol. 1962).

Research output: Chapter in Book/Report/Conference proceedingChapter

Min, B & Choi, I-G 2019, Practical guide for fungal gene prediction from genome assembly and RNA-seq reads by FunGAP. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1962, Humana Press Inc., pp. 53-64. https://doi.org/10.1007/978-1-4939-9173-0_4
Min B, Choi I-G. Practical guide for fungal gene prediction from genome assembly and RNA-seq reads by FunGAP. In Methods in Molecular Biology. Humana Press Inc. 2019. p. 53-64. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9173-0_4
Min, Byoungnam ; Choi, In-Geol. / Practical guide for fungal gene prediction from genome assembly and RNA-seq reads by FunGAP. Methods in Molecular Biology. Humana Press Inc., 2019. pp. 53-64 (Methods in Molecular Biology).
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