Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly ofMalassezia sympodialis

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Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis

Complete and accurate genome assembly and annotation is a crucial foundation for comparative and functional genomics. Despite this, few complete eukaryotic genomes are available, and genome annotation remains a major challenge. Here, we present a complete genome assembly of the skin commensal yeast Malassezia sympodialis and demonstrate how proteogenomics can substantially improve gene annotati...

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Mitochondrial genome sequences are available in large number and new sequences become published nowadays with increasing pace. Fast, automatic, consistent, and high quality annotations are a prerequisite for downstream analyses. Therefore, we present an automated pipeline for fast de novo annotation of mitochondrial protein-coding genes. The annotation is based on enhanced phylogeny-aware hidde...

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Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have de...

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One of the objectives of genome science is the discovery and accurate annotation of all protein-coding genes. Proteogenomics has emerged as a methodology that provides orthogonal information to traditional forms of evidence used for genome annotation. By this method, peptides that are identified via tandem mass spectrometry are used to refine protein-coding gene models. Namely, these peptides a...

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ژورنال

عنوان ژورنال: Nucleic Acids Research

سال: 2017

ISSN: 0305-1048,1362-4962

DOI: 10.1093/nar/gkx006