EAnnot: A genome annotation tool using experimental evidence

Li, Ding; Sabo, Aniko; Berkowicz, Nicolas; Meyer, Rekha; Shotland, Yoram; Johnson, Mark R.; Pepin, Kymberlie H.; Wilson, Richard K.; Strouboulis, John

doi:10.1101/gr.3152604

Cited by 19 publications

(10 citation statements)

References 30 publications

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“…The masked assembly was used to call genes. In total, 38,768 protein coding sequences were predicted using the assembly contigs through a 6-tier gene-calling pipeline(Ding et al 2004). ..…”

Section: Methodsmentioning

confidence: 99%

Gene expression analysis distinguishes tissue-specific and gender-related functions among adult Ascaris suum tissues

Wang¹,

Gao²,

Martin³

et al. 2013

Mol Genet Genomics

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Over a billion people are infected by Ascaris spp. intestinal parasites. To clarify functional differences among tissues of adult A. suum, we compared gene expression by various tissues of these worms by expression microarray methods.. The A. suum genome was sequenced and assembled to allow generation of microarray elements. Expression of over 40,000 60-mer elements was investigated in a variety of tissues from both male and female adult worms. Nearly 50 percent of the elements for which signal was detected exhibited differential expression among different tissues. The unique profile of transcripts identified for each tissue clarified functional distinctions among tissues, such as chitin binding in the ovary and peptidase activity in the intestines. Interestingly, hundreds of gender-specific elements were characterized in multiple nonreproductive tissues of female or male worms, with most prominence of gender differences in intestinal tissue. A. suum genes from the same family were frequently expressed differently among tissues. Transcript abundance for genes specific to A. suum, by comparison to Caenorhabditis elegans, varied to a greater extent among tissues than for genes conserved between A. suum and C. elegans. Analysis using C. elegans protein interaction data identified functional modules conserved between these two nematodes, resulting in identification of functional predictions of essential subnetworks of protein interactions and how these networks may vary among nematode tissues. A notable finding was very high module similarity between adult reproductive tissues and intestine. Our results provide the most comprehensive assessment of gene expression among tissues of a parasitic nematode to date.

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“…The masked assembly was used to call genes. In total, 38,768 protein coding sequences were predicted using the assembly contigs through a 6-tier gene-calling pipeline(Ding et al 2004). ..…”

Section: Methodsmentioning

confidence: 99%

Gene expression analysis distinguishes tissue-specific and gender-related functions among adult Ascaris suum tissues

Wang¹,

Gao²,

Martin³

et al. 2013

Mol Genet Genomics

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“…Genes can be predicted using several evidence-based prediction programs, such as Genewise (Birney et al . 2004), FGENESH_PLUS (Salamov and Solovyev, 2000), Eannot (Ding et al . 2004), and ab initio predictions, such as Fgenesh (Salamov and Solovyev, 2000), GeneMark (Besemer and Borodovsky, 2005) and Snap (Korf, 2004) and the Ensembl annotation pipeline (Clamp et al .…”

Section: The Genome Sequencing Processmentioning

confidence: 99%

“…Generally, a combined approach is used to minimize the number of occasions on which different gene prediction algorithms give different results for the same region of the genome. Genes can be predicted using several evidence-based prediction programs, such as Genewise (Birney et al 2004), FGENESH_PLUS (Salamov and Solovyev, 2000), Eannot (Ding et al 2004), and ab initio predictions, such as Fgenesh (Salamov and Solovyev, 2000), GeneMark (Besemer and Borodovsky, 2005) and Snap (Korf, 2004) and the Ensembl annotation pipeline (Clamp et al 2003). The available ESTs from T. spiralis (Mitreva et al 2004) will provide valuable information when used via the evidence-based gene prediction algorithms to determine exon/intron and gene boundaries as well as splice-isoforms.…”

Section: The Genome Sequencing Processmentioning

confidence: 99%

Advances in the sequencing of the genome of the adenophorean nematodeTrichinella spiralis

Mitreva

Jasmer

2008

Parasitology

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SUMMARY The adenophorean nematodes are evolutionarily distant from other species in the phylum Nematoda. Interspecific comparisons of predicted proteins have supported such an ancient divergence. Accordingly, Trichinella spiralis represents a basal nematode representative for genome sequencing focused on gaining a deeper insight into the evolutionary biology of nematodes. In addition, molecular characteristics that are conserved across the phylum could be of great value for control strategies with broad application. In this review, we describe and summarize progress that has been made on the sequencing and analysis of the T. spiralis genome. The genome sequence was used in preliminary analyses for the investigation of specific questions relating to the biology of T. spiralis and, more generally, to parasitic nematodes. For instance, we evaluated an unusually large DNase II-like protein family, predicted proteins of prospective interest in the parasite-host muscle cell interaction, anthelmintic targets and prospective intestinal genes, the encoded proteins (potentially) linked to immunological control against other nematodes. The results are discussed in relation to characteristics that are broadly conserved among evolutionary distant nematodes. The results lead to expectations that this genome sequence will contribute to advances in research on T. spiralis and other parasitic nematodes.

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“…The masked assembly was used to call genes. In total, 5,538 genes were identified through a 6-tier gene-calling pipeline [19]. In addition, of the 3,840 genes that were identified by our previous A. caninum EST approach [8] 3,589 (represented by 4,816 contig consensus sequences) were not incorporated in calling genes, and therefore added to the list of identified unique genes.…”

Section: Introductionmentioning

confidence: 99%

The canine hookworm genome: Analysis and classification of Ancylostoma caninum survey sequences

Abubucker

Martin

Yin

et al. 2008

Molecular and Biochemical Parasitology

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Hookworms infect nearly a billion people. The Ancylostoma caninum hookworm of canids is a model for studying human infections and information from its genome coupled with functional genomics and proteomics can accelerate progress towards hookworm control. As a step towards a full-scale A. caninum genome project, we generated 104,000 genome survey sequences (GSSs) and determined the genome size of the canine hookworm. GSSs assembled into 57.6 Mb of unique sequence from a genome that we estimate by flow cytometry of isolated nuclei to be 347±1.2 Mb, substantially larger than other Rhabditina species. Gene finding identified 5,538 genes in the GSS assembly, for a total of 9,113 non-redundant A. caninum genes when EST sequences are also considered. Functional classifications of many of the 70% of genes with homology to genes in other species are provided based on Gene Ontology and KEGG associations and secreted and membrane-bound proteins are also identified. Keywordshookworm; Ancylostoma caninum; genome survey sequences; expressed sequence tags; genome; comparative genomics Hookworms are parasitic nematodes that live in the host small intestine and affect mammals including humans, dogs, and cats. Ancylostoma duodenale and Necator americanus infect close to a billion people [1] causing anemia and malnutrition, and also diminished physical and cognitive development in children. A. caninum is a hookworm species that infects canids and is commonly used as a model for studying human infections. Hookworm infections are usually *Corresponding Author: Tel: +1-314-2861118; Fax: +1-314-2861810, E-mail address: mmitreva@watson.wustl.edu (M. Mitreva). Note: Nucleotide sequences data reported in this paper are available in the GenBank, EMBL and DDBJ databases under the accession numbers CW698017 -CW717115, CW958972 -CW978588, CZ194948 -CZ250652.Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. , our recent genome size estimate using flow sorted nuclei surprisingly revealed a genome more than six times this size. Genome size was estimated by prodidium iodide staining and flow cytometry of isolated nuclei following methods described in [10]. To prepare the nuclei, the A. caninum L3s were washed in cold Galbraith buffer pH 7.2 and then pipetted into a plastic petri dish along with 30-50 μl cold Galbraith buffer and chopped (50 times) with a fresh single edge razor blade. The chopped material was washed into one edge of the (tilted) petri dish using an additional 1 ml of cold Galbraith buffer (per liter: 4.26g MgCl2, 8.84 g sodium citrate, 4.2 g [N-morpholino] propane sulfonic acid, 1m...

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EAnnot: A genome annotation tool using experimental evidence

Cited by 19 publications

References 30 publications

Gene expression analysis distinguishes tissue-specific and gender-related functions among adult Ascaris suum tissues

Gene expression analysis distinguishes tissue-specific and gender-related functions among adult Ascaris suum tissues

Advances in the sequencing of the genome of the adenophorean nematodeTrichinella spiralis

The canine hookworm genome: Analysis and classification of Ancylostoma caninum survey sequences

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