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

Abstract

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 user-friendly navigation through the site, a necessity due to the explosion of data from next-generation sequencing platforms. Organism-centric portals containing dynamically generated data are available for over 56 different nematode species. Next-generation data has been added to the various data-mining portals hosted, including NemaBLAST and NemaBrowse. The NemaPath metabolic pathway viewer builds associations using KOs, rather than ECs to provide more accurate and fine-grained descriptions of proteins. Two new features for data analysis and comparative genomics have been added to the site. NemaSNP enables the user to perform population genetics studies in various nematode populations using next-generation sequencing data. HelmCoP (Helminth Control and Prevention) as an independent component of Nematode.net provides an integrated resource for storage, annotation and comparative genomics of helminth genomes to aid in learning more about nematode genomes, as well as drug, pesticide, vaccine and drug target discovery. With this update, Nematode.net will continue to realize its original goal to disseminate diverse bioinformatic data sets and provide analysis tools to the broad scientific community in a useful and user-friendly manner.

Figure 1.

Information flow on Nematode.net. The flowchart outlines the passage of information from raw data to analysis and output onto Nematode.net. New features (boxed in red) as well as resources with data added since the 2008 revision (boxed in blue) have also been indicated.

Figure 2.

Species-centric portal. (A) This species-centric portal screenshot demonstrates the expanding menu bar on the left and shows a screen shot of the species-centric portal for C. elegans. The dynamically generated information for C. elegans includes an image, common name, clade, disease, sequencing data, contact person, BLAST results and KEGG associations. The links can be followed to acquire the desired information. (B) An example of the NCBI's Bioproject page (http://www.ncbi.nlm.nih.gov/bioproject?term=PRJNA72363).

Figure 3.

Transcript assemblies using next-generation sequencing data. (A) Transcript assembly downloads are accessible through this page. The text links can be followed to download the isotig nucleic acid fasta, isotig amino acid fasta, isogroup membership and read membership. The species can be expanded to obtain various assembly statistics and for information regarding the raw data used to assemble the sequences. (B) Putative isoforms (isotigs) built from contigs (which are labeled 1–5). This image shows examples of alternatively spliced transcripts that a user can generate using the cDNA isotig/isogroup information provided. (C) Alignment of a putative gene (isogroup) from A. caninum against a portion of the A. caninum draft genome. Acan_isogroup00809 has two alternatively spliced isotigs, Acan_isotig04444 and Acan_isotig04445 from three contigs. The contig which is present only in one isotig and the genome but not in the other isotig is outlined.

Figure 4.

NemaSNP viewer. This screen shot shows a typical SNP annotation using GBrowse. This example shows a screen shot of SNPs in T. circumcincta (contig02609) in an inbred versus field population represented with triangles along the contig (red triangles indicate non-synonymous, green indicate synonymous SNPs, yellow is a site with multiple alleles that can result in a silent or non-synonymous change, and in blue is a site that lies outside of validated CDS). The inbred and field alignments are shown below the SNP annotation.

Figure 5.

Stage-based metabolic profiling of O. dentatum. KEGG module M00027 (GABA (gamma-Aminobutyrate) shunt) from the pathway Alanine, Aspartate and glutamate Metabolism is shown with a plot displaying stage specific expression. This module was found to be significantly abundant in males, females and the L4 stage in O. dentatum.