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Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes

T. Wylie
2004 Nucleic Acids Research  
Nematode.net (www.nematode.net) is a web accessible resource for investigating gene sequences from nematode genomes.  ...  The longterm goal of nematode.net is to provide the scientific community with the highest quality sequence information and tools for studying these diverse species.  ...  Addi tional useful features of nematode.net Table 1. Nematode EST projects by species SEQUENCES FROM PARASITIC NEMATODES TOP ABSTRACT INTRODUCTION SEQUENCES FROM PARASITIC...  ... 
doi:10.1093/nar/gkh010 pmid:14681448 pmcid:PMC308745 fatcat:alqmlkbvfng3zm36kcgfknephu

Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data

J. Martin, S. Abubucker, E. Heizer, C. M. Taylor, M. Mitreva
2011 Nucleic Acids Research  
Nematode.net (http://nematode.net) has been a publicly available resource for studying nematodes for over a decade.  ...  In the past 3 years, we reorganized Nematode.net to provide more userfriendly navigation through the site, a necessity due to the explosion of data from next-generation sequencing platforms.  ...  group at the TGI for the cDNA library construction and sequencing.  ... 
doi:10.1093/nar/gkr1194 pmid:22139919 pmcid:PMC3245159 fatcat:3cg4tlli5ree3lmiz54chz5ngi

Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics

J. Martin, S. Abubucker, T. Wylie, Y. Yin, Z. Wang, M. Mitreva
2009 Nucleic Acids Research  
and Mitreva, Makedonka, ,"Nematode.net update 2008: Improvements enabling more efficient data mining and comparative nematode genomics. ABSTRACT Nematode  ...  Using tools implemented within Nematode.net, comparative studies were made among intestinal genes from the two parasites and the free-living bacterivore C. elegans.  ...  , animal parasites and free-living species.  ... 
doi:10.1093/nar/gkn744 pmid:18940860 pmcid:PMC2686480 fatcat:ljorexfsrjf7xlgijjkpyvvcha

NemaPath: online exploration of KEGG-based metabolic pathways for nematodes

Todd Wylie, John Martin, Sahar Abubucker, Yong Yin, David Messina, Zhengyuan Wang, James P McCarter, Makedonka Mitreva
2008 BMC Genomics  
Nematode.net http://www.nematode.net is a web-accessible resource for investigating gene sequences from parasitic and free-living nematode genomes.  ...  Description: Here we present the NemaPath pathway server, a web-based pathway-level visualization tool for navigating putative metabolic pathways for over 30 nematode species, including 27 parasites.  ...  The NemaPath project is supported by US National Institute for Allergy and Infectious Disease grant AI46593.  ... 
doi:10.1186/1471-2164-9-525 pmid:18983679 pmcid:PMC2588608 fatcat:gek5pi4yyfbcpagyizlmxog5hi

NEMBASE4: The nematode transcriptome resource

Benjamin Elsworth, James Wasmuth, Mark Blaxter
2011 International Journal of Parasitology  
NEMBASE4 presents a single portal into extensively functionally annotated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal parasites and free-living taxa.  ...  Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services.  ...  JW is supported by a Restracomp Fellowship awarded by the Hospital for Sick Children, Toronto, Canada.  ... 
doi:10.1016/j.ijpara.2011.03.009 pmid:21550347 fatcat:l5ypi67fkzcnfn4mk45fotxy6y

Molecular determinants archetypical to the phylum Nematoda

Yong Yin, John Martin, Sahar Abubucker, Zhengyuan Wang, Lucjan Wyrwicz, Leszek Rychlewski, James P McCarter, Richard K Wilson, Makedonka Mitreva
2009 BMC Genomics  
Majority of the 462 families that were conserved among both free-living and parasitic species contained members from multiple nematode clades, yet ~90% of the 296 parasite-specific families originated  ...  Most nematodes are free-living animals, but many are parasites of plants and animals including humans, posing major ecological and economical challenges around the world.  ...  The parasitic nematode EST sequencing and the Nematode.net at the Genome Center is in part supported by the US National Institute for Allergy and Infectious Disease grant to M.M.  ... 
doi:10.1186/1471-2164-10-114 pmid:19296854 pmcid:PMC2666764 fatcat:2pgmzjsbwzcp7hi23xio7nelfq

Rendering the Intractable More Tractable: Tools from Caenorhabditis elegans Ripe for Import into Parasitic Nematodes

J. D. Ward
2015 Genetics  
Current tools in three commonly studied parasites (Strongyloides spp., Brugia malayi, and Ascaris suum) are described, as are tools from C. elegans that are ripe for adaptation and the benefits and barriers  ...  I review how development of nonparasitic nematodes as genetic models informs efforts to import tools into parasitic nematodes.  ...  Nematode.net (Wylie et al. 2004; Martin et al. 2015) , and WormBase ParaSite provide useful tools for navigating these sequences.  ... 
doi:10.1534/genetics.115.182717 pmid:26644478 pmcid:PMC4676526 fatcat:aro6utdzinabhimkqyjlurnagu

Signatures of adaptation to plant parasitism in nematode genomes

DAVID McK. BIRD, JOHN T. JONES, CHARLES H. OPPERMAN, TAISEI KIKUCHI, ETIENNE G. J. DANCHIN
2014 Parasitology  
In this review, we report genomic features and characteristics that appear to be common in plant-parasitic nematodes while absent or rare in animal parasites, predators or free-living species.  ...  S U M M A R Y Plant-parasitic nematodes cause considerable damage to global agriculture.  ...  Genomes and transcriptomes of plant-parasitic nematodes The genome sequence of the free-living nematode C. elegans was released in 1998 and was the first animal genome sequenced (The C. elegans Genome  ... 
doi:10.1017/s0031182013002163 pmid:25656361 pmcid:PMC4413825 fatcat:kig2lntrdbfzxpvkpgugagupdu

APlasmodium-like virulence effector of the soybean cyst nematode suppresses plant innate immunity

Jason B. Noon, Mingsheng Qi, Danielle N. Sill, Usha Muppirala, Sebastian Eves-van den Akker, Thomas R. Maier, Drena Dobbs, Melissa G. Mitchum, Tarek Hewezi, Thomas J. Baum
2016 New Phytologist  
A Plasmodium-like virulence effector of the soybean cyst nematode suppresses plant innate immunity Noon, Jason B.; Qi, Mingsheng; Sill, Danielle N.; Muppirala, Usha; Eves-van den Akker, Sebastian; Maier  ...  This work was supported by a grant from the Iowa Soybean Association and USDA-NIFA-AFRI Award  ...  Acknowledgements This is a Journal Paper of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa, supported by Hatch Act and State of Iowa funds.  ... 
doi:10.1111/nph.14047 pmid:27265684 fatcat:x53womnw2ngkrfa5whwuux2nbm

Abstracts of Special Session Presentations at the 2000 APS Annual Meeting

2000 Phytopathology  
The web-accessible resource Nematode.net (www.nematode.net) provides access to genome data specific to free-living and parasitic nematodes.  ...  The course I taught with my husband (John Ferris) was called Fundamentals of Nematology and included free-living nematodes and animal parasites as well as plant nematodes.  ... 
doi:10.1094/phyto.2000.90.6.s91 pmid:18944404 fatcat:tnypmhcptffodflusrtyekokge

Bioinformatics tools and analysis to identify candidate lethal genes in Root-knot nematode (RKN) and its comparison with soybean cyst nematode (SCN) infection in soybean

Ahmed I. Ismail
2013
To that end we compared RKN gene sequences to the well-characterized and fully sequenced genome of the free-living nematode C. elegans (Caenorhabditis elegans).  ...  The RKN sequences were obtained from nematode.net. Our analysis yielded many candidate lethal genes between Meloidogyne spp. and C.elegans.  ...  While Nematode.net started as a project site, over the years it became a community resource dedicated to the study of parasitic nematodes.  ... 
doi:10.13016/m2w704 fatcat:vaewlbdmkzgdxbfiqhlbr4b53i

Tools and Techniques for Genome Annotation and Analysis

Carson Hinton Holt
2014
Annotations produced by MAKER2 can be directly loaded into many popular downstream annotation analysis and management tools from the Generic Model Organism Database Project.  ...  , which creates new difficulties for data integration and management that are not well addressed by existing tools.  ...  It is a protostome and a free-living Analysis of the repeats showed that the S. mediterranea genome is A/T rich, with low-complexity regions comprising 22% of all sequence, and high-complexity dispersed  ... 
doi:10.26053/0h-xcfx-3vg0 fatcat:b7lchjg4sreb5gfbkfcyunuqeq