An empirical analysis of training protocols for probabilistic gene finders

Majoros, William H.; Salzberg, Steven L.

doi:10.1186/1471-2105-5-206

Cited by 24 publications

(6 citation statements)

References 28 publications

(25 reference statements)

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“…AUGUSTUS for maize is used for the Poaceae family. For GeneZilla, we employed an automatic training program, GRAPE ( Majoros and Salzberg 2004 ). To train the other programs, we followed the instructions provided by the software developer.…”

Section: Methodsmentioning

confidence: 99%

MEGANTE: A Web-Based System for Integrated Plant Genome Annotation

Numa¹,

Itoh²

2013

Plant and Cell Physiology

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The recent advancement of high-throughput genome sequencing technologies has resulted in a considerable increase in demands for large-scale genome annotation. While annotation is a crucial step for downstream data analyses and experimental studies, this process requires substantial expertise and knowledge of bioinformatics. Here we present MEGANTE, a web-based annotation system that makes plant genome annotation easy for researchers unfamiliar with bioinformatics. Without any complicated configuration, users can perform genomic sequence annotations simply by uploading a sequence and selecting the species to query. MEGANTE automatically runs several analysis programs and integrates the results to select the appropriate consensus exon–intron structures and to predict open reading frames (ORFs) at each locus. Functional annotation, including a similarity search against known proteins and a functional domain search, are also performed for the predicted ORFs. The resultant annotation information is visualized with a widely used genome browser, GBrowse. For ease of analysis, the results can be downloaded in Microsoft Excel format. All of the query sequences and annotation results are stored on the server side so that users can access their own data from virtually anywhere on the web. The current release of MEGANTE targets 24 plant species from the Brassicaceae, Fabaceae, Musaceae, Poaceae, Salicaceae, Solanaceae, Rosaceae and Vitaceae families, and it allows users to submit a sequence up to 10 Mb in length and to save up to 100 sequences with the annotation information on the server. The MEGANTE web service is available at https://megante.dna.affrc.go.jp/.

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Section: Methodsmentioning

confidence: 99%

MEGANTE: A Web-Based System for Integrated Plant Genome Annotation

Numa¹,

Itoh²

2013

Plant and Cell Physiology

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“…We also used three methods to annotate genes in the genome, including the de novo prediction, homology-based prediction, and transcriptome-based prediction were combined using EvidenceModeler (EVM) v1.1.1 (Haas et al, 2008) and PASA v2.4.0 (Haas et al, 2008). For de novo gene predictions, we used Augustus v3.4.0 (Stanke et al, 2008), Genscan v3.1 (Burge and Karlin, 1998), and GlimmerHMM v3.0.1 (Majoros and Salzberg, 2004) to analyze the repeat-masked genome. For homology-based predictions, the protein sequences of Cynoglossus semilaevis, Danio rerio, Gasterosteus aculeatus, Gadus morhua, Larimichthys crocea, Oryzias latipes, Oreochromis niloticus, T. rubripes, T. bimaculatus and Tetraodon nigroviridis obtained from NCBI were aligned to the yellow boxfish genome by following the pipeline of Chen et al (Chen et al, 2019).…”

Section: Genome Annotationmentioning

confidence: 99%

Chromosome-level genome assembly of the yellow boxfish (Ostracion cubicus) provides insights into the evolution of bone plates and ostracitoxin secretion

et al. 2023

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The Ostracion cubicus, commonly known as the yellow boxfish, is a remarkable species with a body encased in a bone plate and the ability to produce an ostracitoxin from their skin when under stress. However, the genetic basis of those effective defense traits is still largely unknown due to the lack of genomic resources. Here, we assembled the first chromosome-level genome of O. cubicus with 867.50 Mb in genome size and 34.86 Mb N50 scaffold length by HiFi and Hi-C sequencing. Twenty-five pseudo-chromosomes, numbered according to size, covered 94.13% of the total assembled sequences. A total of 23,224 protein-coding genes were predicted, with a BUSCO completeness of 98.6%. Positive selection or rapid evolution was observed in genes related to scale and bone development (acsl4a, casr, keap1a, tbx1), and up-regulation of transcription was found in the skin of boxfish (bmp1, bmp2k, bmp4, bmp7, smad5, suco, prelp, mitf), likely associated with the bone plates evolution in the yellow boxfish. An expansion of the solute carrier family 22, a cluster of genes in solute carrier (SLCs) family, transmembrane protein family (TMEMs), vesicle trafficking (SECs), ATP-binding cassette (ABCs) and apolipoproteins (APOs) were identified under positive selection, rapid evolution, or up-regulated in the skin of boxfish, likely associated with the ostracitoxin secretion in the yellow boxfish. Our study not only presents a high-quality boxfish genome but also provides insights into bone plates evolution and ostracitoxin secretion of O. cubicus.

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“…For RNA-seq data, we first used HISAT v2.1.0 (Kim et al, 2015) with default parameters to align RNA-seq data to V. variegatus genome and then used StringTie v2.0 (Pertea et al, 2015) with default parameters to reconstruct transcripts. After using RepeatMasker to mask TEs of the assembled genome, five de novo gene predictors, including Augustus (Stanke et al, 2008), GlimmerHMM (Majoros and Salzberg, 2004), SNAP (Korf, 2004), Geneid (Alioto et al, 2018) and Genscan (Burge and Karlin, 1998), were used for gene prediction. For the homologybased prediction, proteins sequences of Homo sapiens, Danio rerio, Oryzias latipes, Takifugu rubripes, Cynoglossus semilaevis, Scophthalmus maximus and Gasterosteus aculeatus were downloaded from Ensembl (release 98), Paralichthys olivaceus proteins were downloaded from NCBI, then we used Exonerate v2.2 (Slater and Birney, 2005) (identity>80%) to map the proteins sequences to V. variegatus genome for conduct homology-based gene prediction.…”

Section: Gene Structure and Functional Annotationmentioning

confidence: 99%