PERFORM Publications

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Title		Authors	PubMed ID
1	Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulans.	Bastos RW, Valero C, Silva LP, Schoen T, Drott M, Brauer V, Silva-Rocha R, Lind A, Steenwyk JL, Rokas A, Rodrigues F, Resendiz-Sharpe A, Lagrou K, Marcet-Houben M, Gabaldón T, McDonnell E, Reid I, Tsang A, Oakley BR, Loures FV, Almeida F, Huttenlocher A, Keller NP, Ries LNA, Goldman GH	32269156 CSFG
2	mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support.	Strasser K, McDonnell E, Nyaga C, Wu M, Wu S, Almeida H, Meurs MJ, Kosseim L, Powlowski J, Butler G, Tsang A	25754864 CSFG
3	Manual Gene Curation and Functional Annotation.	McDonnell E, Strasser K, Tsang A	29876819 CSFG
4	Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri.	Vesth TC, Nybo JL, Theobald S, Frisvad JC, Larsen TO, Nielsen KF, Hoof JB, Brandl J, Salamov A, Riley R, Gladden JM, Phatale P, Nielsen MT, Lyhne EK, Kogle ME, Strasser K, McDonnell E, Barry K, Clum A, Chen C, LaButti K, Haridas S, Nolan M, Sandor L, Kuo A, Lipzen A, Hainaut M, Drula E, Tsang A, Magnuson JK, Henrissat B, Wiebenga A, Simmons BA, Mäkelä MR, de Vries RP, Grigoriev IV, Mortensen UH, Baker SE, Andersen MR	30349117 CSFG
5	The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi.	Aguilar-Pontes MV, Brandl J, McDonnell E, Strasser K, Nguyen TTM, Riley R, Mondo S, Salamov A, Nybo JL, Vesth TC, Grigoriev IV, Andersen MR, Tsang A, de Vries RP	30425417 CSFG
6	Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli	Mäkelä MR; DiFalco M; McDonnell E; Nguyen TTM; Wiebenga A; Hildén K; Peng M; Grigoriev IV; Tsang A; de Vries RP;	30487660 CSFG

Title:	Manual Gene Curation and Functional Annotation.
Authors:	McDonnell E, Strasser K, Tsang A
Link:	https://www.ncbi.nlm.nih.gov/pubmed/29876819?dopt=Abstract
DOI:	10.1007/978-1-4939-7804-5_16
Publication:	Methods in molecular biology (Clifton, N.J.)
Keywords:	Gold-standard genome resource; Manual functional assignment; Manual gene curation; Whole-genome annotation;
PMID:	29876819	Category:	Methods Mol Biol	Date Added:	2019-06-07
Dept Affiliation:	CSFG 1 Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada. 2 Centre for Structural and Functional Genomics, Concordia University, Montreal, QC, Canada. kimchi.strasser@concordia.ca.

Description:

Manual Gene Curation and Functional Annotation.

Methods Mol Biol. 2018;1775:185-208

Authors: McDonnell E, Strasser K, Tsang A

Abstract

No genome sequencing project is complete without structural and functional annotation. Gene models and functional predictions for these models can be obtained relatively easily using computational methods, but they are prone to errors. We describe herein the steps we use to manually curate gene models and functionally annotate them. Our approach is to examine each gene model carefully, and improve its structure if necessary, using a comprehensive set of experimental and computational data as evidence. Then, functional predictions are assigned to the gene models based on conserved protein domains and sequence similarities. We use stringent sequence similarity cutoffs and reviewed sequence-database records as external sources for our annotations. By methodically choosing which evidence to use for each annotation, we minimize the risk of adopting and assigning false predictions to the gene models.

PMID: 29876819 [PubMed - indexed for MEDLINE]

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