PERFORM Publications

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Title		Authors	PubMed ID
1	Using Models to (Re-)Design Synthetic Circuits.	McCallum G, Potvin-Trottier L	33405217 BIOLOGY
2	Computer-Aided Design of Active Pseudoknotted Hammerhead Ribozymes.	Najeh S, Zandi K, Djerroud S, Kharma N, Perreault J	32712917 ENCS
3	Metabolomic and lipidomic analyses of chronologically aging yeast.	Richard VR, Bourque SD, Titorenko VI	25213255 BIOLOGY
4	A Cell-Free Content Mixing Assay for SNARE-Mediated Multivesicular Body-Vacuole Membrane Fusion.	Karim MA, Samyn DR, Brett CL	30317513 BIOLOGY
5	Visualization of SNARE-Mediated Organelle Membrane Hemifusion by Electron Microscopy.	Mattie S, Kazmirchuk T, Mui J, Vali H, Brett CL	30317518 BIOLOGY
6	Identification of Genes Involved in the Degradation of Lignocellulose Using Comparative Transcriptomics.	Gruninger RJ, Reid I, Forster RJ, Tsang A, McAllister TA	28417376 CSFG
7	Isolation and Preparation of Extracellular Proteins from Lignocellulose Degrading Fungi for Comparative Proteomic Studies Using Mass Spectrometry	Robert J Gruninger	28417377 CSFG
8	Introduction: Overview of Fungal Genomics.	de Vries RP, Grigoriev IV, Tsang A	29876804 CSFG
9	Fungal Genomic DNA Extraction Methods for Rapid Genotyping and Genome Sequencing.	Bellemare A, John T, Marqueteau S	29876805 CSFG
10	Mass Spectrometry-Based Proteomics	Marcos Rafael Di Falco	29876812 CSFG
11	Evolutionary Adaptation to Generate Mutants.	de Vries RP, Lubbers R, Patyshakuliyeva A, Wiebenga A, Benoit-Gelber I	29876815 BIOLOGY
12	Manual Gene Curation and Functional Annotation.	McDonnell E, Strasser K, Tsang A	29876819 CSFG
13	Evaluating Programs for Predicting Genes and Transcripts with RNA-Seq Support in Fungal Genomes.	Reid I	29876820 CSFG
14	Phylogenetic Analysis of Protein Family.	Song L, Wu S, Tsang A	29876824 CSFG

Title:	Evaluating Programs for Predicting Genes and Transcripts with RNA-Seq Support in Fungal Genomes.
Authors:	Reid I
Link:	https://www.ncbi.nlm.nih.gov/pubmed/29876820?dopt=Abstract
DOI:	10.1007/978-1-4939-7804-5_17
Publication:	Methods in molecular biology (Clifton, N.J.)
Keywords:	Bioinformatics; Cleaning short sequence reads; Gene prediction; RNA-Seq; Transcript prediction;
PMID:	29876820	Category:	Methods Mol Biol	Date Added:	2019-06-07
Dept Affiliation:	CSFG 1 Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada. ian.reid@concordia.ca.

Description:

Evaluating Programs for Predicting Genes and Transcripts with RNA-Seq Support in Fungal Genomes.

Methods Mol Biol. 2018;1775:209-227

Authors: Reid I

Abstract

The steps needed to computationally predict genes and transcripts in fungal genomes with support from RNA-Seq data are described in detail for three prediction programs: CodingQuarry, BRAKER1, and Harfang. These programs predicted from 86% to 92% (Harfang) of the genes in a manually curated reference set for Aspergillus niger strain NRRL3. Genes with little or no RNA-Seq read coverage were predicted less successfully than genes with adequate coverage.

PMID: 29876820 [PubMed - indexed for MEDLINE]

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