Computational discovery and annotation of conserved small open reading frames in fungal genomes

Mat-Sharani, Shuhaila; Firdaus-Raih, Mohd

doi:10.1186/s12859-018-2550-2

Cited by 22 publications

(9 citation statements)

References 48 publications

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“…Furthermore, the annotation errors are often propagated between species and the more "draft" genomes we produce, the more errors we create and propagate [3][4][5]. Other important challenges that have attracted interest recently include the prediction of small proteins/peptides coded by short open reading frames (sORFs) [26,27] or the identification of events such as stop codon recoding [28]. These atypical proteins are often overlooked by the standard gene prediction pipelines, and their annotation requires dedicated methods or manual curation.…”

Section: Introductionmentioning

confidence: 99%

A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms

et al. 2020

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Background: The draft genome assemblies produced by new sequencing technologies present important challenges for automatic gene prediction pipelines, leading to less accurate gene models. New benchmark methods are needed to evaluate the accuracy of gene prediction methods in the face of incomplete genome assemblies, low genome coverage and quality, complex gene structures, or a lack of suitable sequences for evidence-based annotations. Results: We describe the construction of a new benchmark, called G3PO (benchmark for Gene and Protein Prediction PrOgrams), designed to represent many of the typical challenges faced by current genome annotation projects. The benchmark is based on a carefully validated and curated set of real eukaryotic genes from 147 phylogenetically disperse organisms, and a number of test sets are defined to evaluate the effects of different features, including genome sequence quality, gene structure complexity, protein length, etc. We used the benchmark to perform an independent comparative analysis of the most widely used ab initio gene prediction programs and identified the main strengths and weaknesses of the programs. More importantly, we highlight a number of features that could be exploited in order to improve the accuracy of current prediction tools. Conclusions:The experiments showed that ab initio gene structure prediction is a very challenging task, which should be further investigated. We believe that the baseline results associated with the complex gene test sets in G3PO provide useful guidelines for future studies.

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Section: Introductionmentioning

confidence: 99%

A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms

et al. 2020

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“…Randomly occurring ORFs are unlikely to be preserved through evolution, whereas highly conserved regions are likely to be functional. While bioinformatic analyses have successfully identified functional proteins, many recently published studies report on thousands or even millions of conserved non‐annotated regions (Mat‐Sharani & Firdaus‐Raih, ). However, translated smORFs exhibit a lower degree of evolutionary conservation than known genes (Storz et al., ).…”

Section: Commentarymentioning

confidence: 99%

Proteomic Detection and Validation of Translated Small Open Reading Frames

Khitun

Slavoff

2019

CP Chemical Biology

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Small open reading frames (smORFs) encode previously unannotated polypeptides or short proteins that regulate translation in cis (eukaryotes) and/or are independently functional (prokaryotes and eukaryotes). Ongoing efforts for complete annotation and functional characterization of smORF‐encoded proteins have yielded novel regulators and therapeutic targets. However, because they are excluded from protein databases, initiate at non‐AUG start codons, and produce few unique tryptic peptides, unannotated small proteins cannot be detected with standard proteomic methods. Here,, we outline a procedure for mass spectrometry‐based detection of translated smORFs in cultured human cells from protein extraction, digestion, and LC‐MS/MS, to database preparation and data analysis. Following proteomic detection, translation from a unique smORF may be validated via siRNA‐based silencing or overexpression and epitope tagging. This is necessary to unambiguously assign a peptide to a smORF within a specific transcript isoform or genomic locus. Provided that sufficient starting material is available, this workflow can be applied to any cell type/organism and adjusted to study specific (patho)physiological contexts including, but not limited to, development, stress, and disease. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Protein extraction, size selection, and trypsin digestion Alternate Protocol 1: In‐solution C8 column size selection Support Protocol 1: Chloroform/methanol precipitation Support Protocol 2: Reduction, alkylation, and in‐solution protease digestion Support Protocol 3: Peptide de‐salting Basic Protocol 2: Two‐dimensional LC‐MS/MS with ERLIC fractionation Basic Protocol 3: Transcriptomic database construction Alternate Protocol 2: Transcriptomics database generation with gffread Basic Protocol 4: Non‐annotated peptide identification from LC‐MS/MS data Basic Protocol 5: Validation using isotopically labeled synthetic peptide standards and siRNA Basic Protocol 6: Transcript validation using transient overexpression

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“…In the case of genome annotation, genes encoding small open reading frames are frequently missed. Mat-Sharani and Firdaus-Raih [10] have developed a generic annotation workflow for targeting these elusive regions and applied it successfully to a massive dataset of 31 fungal genomes.…”

Section: Sequence Analysismentioning

confidence: 99%

APBioNet's annual International Conference on Bioinformatics (InCoB) returns to India in 2018

et al. 2019

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InCoB, one of the largest annual bioinformatics conferences in the Asia-Pacific region since its launch in 2002, returned to New Delhi, India after 12 years, with a conference attendance of 314 delegates. The 2018 conference had sessions on Big Data and Algorithms, Next Generation Sequencing and Omics Science, Structure, Function and Interactions, Disease and Drug Discovery and Plant and Agricultural Bioinformatics. The conference also featured an industry track as well as panel discussions on Women in Bioinformatics and Democratization vs. Quality control in academic publishing. Asia Pacific Bioinformatics Interaction & Networking Society (APbians) was launched as an APBionet Special Interest Group. Of the 52 oral presentations made, 22 were accepted in supplemental issues of BMC Bioinformatics, BMC Genomics or BMC Medical Genomics and are briefly reviewed here. Next year's InCoB will be held in Jakarta, Indonesia from September 10-12, 2019.

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Computational discovery and annotation of conserved small open reading frames in fungal genomes

Cited by 22 publications

References 48 publications

A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms

A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms

Proteomic Detection and Validation of Translated Small Open Reading Frames

APBioNet's annual International Conference on Bioinformatics (InCoB) returns to India in 2018

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