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[Sept.19.2014]   
Nematode.net has grown again, click here to learn more!

[Sept.15.2014]   
Nematode.net is now part of the Helminth.net collection of sites, click here to learn more!





What paper to cite when using this website?
For citing results and publications form this website, please use:

Martin J., Abubucker S., Wylie T., Yin Y., Wang Z. and Mitreva M. (2009) Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics Nucleic Acids Research 37 (suppl 1): D571-D578

Wylie T., Martin J., Dante M., Mitreva M., Clifton S.C., Chinwalla A., Waterston R.H., Wilson R.K. and McCarter J.P. (2004) Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes Nucleic Acids Research 32 (suppl 1): D423-D426

What is nematode.net, who maintains it, and how did it start?
Nematode.net is the home page of the parasitic nematode EST project at The Genome Institute at Washington University in St. Louis. The site was established in 2000 as a component of the NIH-NIAID grant "A Genomic Approach to Parasites from the Phylum Nematoda". While Nematode.net started as a project site, over the years it became a community resource dedicated to the study of parasitic nematodes. The site is the property of Washington University.

What are nematodes and why do they matter?
Nematodes are unsegmented round worms. In terms of individuals, nematodes account for an estimated four of every five animals in the world (The other fifth are mostly beetles). There are 10,000 known species and the actual number may be more than 100,000. While most nematodes are free-living, parasitic nematodes pose major challenges to human health and agriculture. Parasitic nematodes, including whipworm, Ascaris, hookworm, and filarial worms, currently infect about 3 billion people. Plant parasitic nematodes, such as root knot nematode, cause an estimated 80 billion dollars in crop damage annually. The free-living nematode C. elegans has been used extensively since the late 1960s as a genetic model organism and is among the most completely characterized of all metazoans. The C. elegans genome was the first comprehensively sequenced metazoan genome (1998).

What are ESTs/cDNAs and why are they being generated?
Expressed sequence tags (ESTs) are single pass sequences from cDNA clones using Sanger/ABI sequencing platform. They provide partial sequences corresponding to messenger RNAs and provide a rapid and cost-effective method for initial characterization of genomes. However, they tend to be redundant and do not provide information about non-exonic sequences or genome organization. ESTs can be used to identify individual genes within parasitic nematodes. Such genes can be targets for anthelmintics, vaccines, or nematicides. Gene sequences are also critical reagents for most molecular studies of an organism. Most ESTs being generated for the TGI's parasitic nematode project are 5' reads. Some libraries are generated by PCR using the nematode transplice leader SL1, thereby ensuring that the 5' end is sequenced. Other libraries are directionally cloned but without selection for a splice leader.

Due to the proliferation of large-scale DNA-sequencing projects in recent years, alternative sequencing methods to reduce time and cost have become available. One such 'massively parallel' sequencing platform is the FLX GS20 sequencer from 454 Life Sciences. This is a sequencing system that offers a 100-fold increase in throughput over the current state-of-the-art Sanger sequencing technology on capillary electrophoresis instruments. Therefore, our recent cDNA sequencing is performed using the GS FLX pyrosequencers. We use distinct pipelines for the analysis of ABI and FLX sequences including different methods for basecalling, linker trimming, low complexity region and contaminant screening, and return of high-quality sequences (Mitreva and Mardis, 2009; Methods Mol Biol. 2009;533:153-87). The generated sequences are often of varying length and quality and their integration requires algorithms that can handle the differences.

How are collaborations established?
In total, 30 collaborations have been established with investigators internationally, providing access to material from collected nematodes. Species have been selected for 1) medical or economic importance, 2) use as an accessible system for studies with an interested scientific community, 3) distribution across the phyla Nematoda. Individuals interested in establishing collaborations should contact Makedonka Mitreva (mmitreva@genome.wustl.edu).

How do I make use of the various tools presented
HelmCoP gene search Search the HelmCoP database for genes using supported queries. For information regarding gene naming for specific species, please refer to the HelmCoP FAQ. A typical HelmCoP user will first build a list of genes for the organism(s) they are interested in using the various filters provided. Genes of interest can be further explored by identifying the ortholog in which a given gene resides, and copy-pasting that ortholog name into a search constructed on the HelmCoP orthologs page. In this manner related genes meeting your filters can be found. HelmCoP can be searched using GO annotations, KEGG orthology (KO), and Interpro domains. Essentiality can also be used in the search to find genes that have RNAi phenotypes based on association with C. elegans genes. Genes with a PDB structure, signal peptide and a particular DrugBank ID can also be found. Further, HelmCoP can be searched for genes that are potential vaccine candidates. HelmCoP also provides extensive annotation of included proteins (see the chart at the bottom of this page). Output is originally displayed in HTML format, but a tab-delimited version of your query output is available via the Full Results Download button at the top of the results page. Please refer to the HelmCoP FAQ for additional information.

HelmCoP ortholog search This page gives the user access to orthology and homology information for genes of interest. The database of helminth proteomes is the most comprehensive available to date with 38,776 orthologous groups from 18 species. Orthology was inferred using OrthoMCL (Li, L Genome Res. 13:2178-2189). The user can require that a certain species be included in an orthologous group, while excluding another species from a search, enabling the user to isolate groups of proteins found in a select group of species. HelmCoP can also be searched using GO annotations, KEGG orthology (KO), and Interpro domains. Essentiality can also be used in the search to find genes that have RNAi phenotype, based on association with C. elegans genes. Genes with a PDB structure, signal peptide and a particular DrugBank ID can also be found. Further, HelmCoP can be searched for genes that are potential vaccine candidates. HelmCoP also provides extensive annotation of included proteins (see chart at the bottom of this page). Using orthology, annotation can be carefully expanded to other proteins in an orthologous group, yielding many new insights into proteins with limited information. The page provides insights into gene duplications, deletions, and insertions. This page is particularly useful for comparative genomics and drug discovery. Output is originally displayed in HTML format, but a tab-delimited version of your query output is available via the Full Results Download button at the top of the results page. Please refer to the HelmCoP FAQ for additional information.

NemaBLAST vs. reads grouped by library NemaBLAST vs reads grouped by library is typically used to search for your sequence of interest amongst a custom selection of libraries from species of interest. For example, you may search your query against Trichinella spiralis cDNAs, but exclude all libraries except the adult libraries "Trichinella spiralis adult pAMP1 v1" and "Trichinella spiralis adult SL1 TOPO v1".

NemaBLAST vs. EST contigs & genes NemaBLAST vs EST contigs & genes is typically used to screen for the presence or absence of your query across a spectrum of organisms.

NemaGene cluster search Most access into the NemaGene database comes from other tools within the Nematode.net site such as the contig links from NemaPath which directly jump to the contig details pages that are the terminus of a NemaGene search. But the NemaGene cluster search form can also be of use when you have identified a contig, isotig or gene from some other Nematode.net resources (eg. a pan-phylum NemaBLAST result or a cluster of interest from our FTP service) and want more detail on that sequence entity. Another common use would be identifying a stage specific set of isotigs/contigs for a given organism using the 'Stage' search selection.

NemaSNP Uses for this information will vary depending on the experiment described, its state of annotation, and the quality of the assembly. For well-annotated assemblies, this tool can highlight genes that differ between distinct populations of worms, for example a drug-resistant population versus a normal population. For less-annotated (or unannotated) assemblies, this tool can point out contigs that may contain features that differentiate the populations for further study.

GO Associations AmiGO provides a means to identify available transcript resources for a given biological process, cellular component or molecular function of interest. The pie-charts provided at every node give a quick view of how much worm data is available under that term, and by clicking on the term itself you are presented with contig names mapping into that term, which can be used to search NemaGene for more information on that transcript assembly contig*.
*note: contig names in AmiGO are extended versions of the NemaGene contig names. To search for a contig name in NemaGene, just use the first 7 characters of the name (eg. AE00825 rather than AE00825_p10_2).

NemaPath KEGG Associations NemaPath provides information about the presence, absence and composition of enzymatic pathways in given organisms based on actual transcript data and allows for the comparison of any two organisms represented in the database. It also provides higher-order comparisons across clades and hosts. This is useful in many ways, from identifying potential drug targets to helping understand the differences between species utilizing different survival strategies. Browsing the clade- or host- specific NemaPath comparisons can offer insight into taxa defining differences, while the ability to directly compare any two species in the database provides a direct visualization of enzymatic differences between the two.

Nematode protein families (NemFam) This resource provides access to a pool of conserved regions of nematode-specific proteins. Typical users will either start with a known transcript assembly contig (such as MI04602), or use the Advanced search to comb the NemFam database for families shared amongst their species of interest. After entering your selection, a table is shown listing NemFam families containing members from all your selected species, and describing what annotations are available for each family. The NemFam id (NFid) links provide access to a gbrowse view showing the identified features per family member. This information is useful in many ways. For example a contig you suspect to be partial, without enough sequence to itself successfully be annotated with a signal peptide or transmembrane region, may be found to belong to a family wherein other members do exhibit signal peptides and transmembrane domains, leading you to believe your contig may be secreted.


 
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