• GO associations - Improved information available via AmiGO pages. All GO associations have been updated to GO termdb release 13.1




• NemaPath KEGG associations - Has been updated to KEGG release 40 and tree view has been added for all species. It is possible to highlight a specific EC number on each pathway map from this tree view.




• NemaGene Cluster Blast - The web BLAST server was upgraded to have better performance for multiple, concurrent users and was migrated to new hardware.




• NemaGene Cluster search - The Gbrowse cluster hub pages have been modified and improved.
• Publications: The bandit transposon, a mariner-like mobile genetic element from the genome of the hookworm, Ancylostoma caninum: inferred horizontal transmission between host and parasite ,
  
  Parasitic nematodes - From genomes to control

• NHGRI announces support for the sequencing of 10 parasitic nematode species, members of the order Strongylida;
• New clustered species: Nippostrongylus brasiliensis (7931 ESTs) and Caenorhabditis remanei (21506 ESTs);
• NemaGene Cluster Blast now includes: EST contigs for Xiphinema index and Nippostrongylus brtasiliensis, and GSS contigs for Ancylostoma caninum and Ascaris suum. The GSS assembly contigs, EST contig consensus sequences and corresponding membership files are available at the FTP site;
• NemaPath KEGG associations have been updated to version 40 for 31 species;
• GO association for 29 species have been added;
• Publications: Biology and genome of Trichinella spiralis;
• GBrowse view has been generated for EST clusters of all 29 species along with the NR homologies for each contig, and library information for component ESTs. These cluster 'hubs' have been integrated into Nematode.net via the "NemaGene Cluster Search" page. The cluster page now includes a "View Cluster hub" button that links to the GBrowse view of the related cluster, and once there a link is provided to get the user back to the cluster page. The GBrowse contig features link back to the contig page on Nematode.net, and the individual ESTs themselves link to the sequence entry in GenBank;

• Job opening!  We're looking for another motivated person to join our team. If interested please view the full listing:  Computational biologist CB03


• GO associations pages updated! New AmiGO! browser now in use! New datasets now available for browsing:

  Ancylostoma caninum genes (8805 genes) & Brugia malayi genes (11750 genes)

• New KEGG associations for 8805 Ancylostoma caninum genes

• Clustered 1 new species:

  Nippostrongylus brasiliensis (3949 contigs (comprised of 7931 ESTs) grouped into 2576 clusters)

• New publications:

  Mitreva M, Wendl MC, Martin J, Wylie T, Yin Y, Larson A, Parkinson J, Waterston RH, McCarter JP. 2006 "Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species." Genome Biol. 2006 Aug 14;7(8):R75 [Epub ahead of print]

  Li BW, Rush AC, Weil GJ, McCarter JP, Mitreva M. 2006 "Brugia malayi: effects of radiation and culture on gene expression in infective larvae." Mol Biochem Parasitol. 2006 Oct;149(2):201-7.

  Yin Y, Martin J, McCarter JP, Clifton SW, Wilson RK, Mitreva M. 2006 "Identification and analysis of genes expressed in the adult filarial parasitic nematode Dirofilaria immitis." Int J Parasitol. 2006 Jun;36(7):829-39.

  Mitreva-Dautova M, Roze E, Overmars H, de Graaff L, Schots A, Helder J, Goverse A, Bakker J, Smant G. 2006 "A symbiont-independent endo-1,4-beta-xylanase from the plant-parasitic nematode Meloidogyne incognita." Mol Plant Microbe Interact. 2006 May;19(5):521-9.

• Integration with Wormbase

  Nematode.net contig pages contain links to WormBase where homologies to C.elegans genes were found. From WormBase, C.elegans genes with hits to parasitic nematode contigs have links back to Nematode.net under the "non-elegans ESTs" track in the gbrowse view of the gene.

• Clustered 9 species:

  Meloidogyne arenaria, Toxocara canis, Meloidogyne javanica, Ostertagia ostertagi, Globodera pallida, Meloidogyne parananensis, Heterodera schachtii, Radopholus similis and Parastrongyloides trichosuri

• KEGGv37 viewer for 26 species


• New publications:

  Mitreva, M., J. Appleton, J. P. McCarter, and D. P. Jasmer. 2005. “Expressed Sequence Tags From Life Cycle Stages of Trichinella spiralis: Application to Biology and Parasite Control,” Veterinary Parasitology, 132:13-17.

  Vanholme, B., M. Mitreva, W. V. Criekinge, M. Logghe, J. P. McCarter, and G. Gheysen. 2005. “Detection of Proteins Secreted by the Plant-parasitic Nematode Heterodera schachtii Based on Expressed Sequence Tags Analysis,” Parasitology Research, 98(5):414-24.

  Ben-Wen Li, AC Rush, SD Crosby, W Warren, SA Williams, M. Mitreva, GJ Weil. 2005. Profiling of gender-regulated gene transcripts in the filarial nematode Brugia malayi by cDNA oligonucleotide array analysis. Molecular and Biochemical Parasitology, 143: 49-57.

  Behm, C. A., M. M. Bendig, J. P. McCarter, A. E. Sluder. 2005. “RNA Interference-based Discovery and Validation of New Drug Targets in Filarial Nematodes,” Trends in Parasitology, 21:97-100.

  
  

December,
2005

• New codon usage data added:

Codon Usage Tables
• KEGG associations viewer now available!



(click on the image to jump to the KEGG associations page)

• The Sequence Analyst CB01 position has been filled.


• New Publications:
  

   Comparative genomics of nematodes.
  

• Job opening!  We're looking for another motivated person to join our team. If
  interested please view the full listing:  Sequence Analyst CB01


• Parasitic nematode project sequencing moved beyond generating ESTs. In
  the past few months we have generated 94,429 Ancylostoma caninum and
  19,637 Strongyloides ratti genome survey sequences (GSSs). GSS sequences
  are available from dbGSS division of GenBank.


• New publications:

    An Expressed Sequence Tag Analysis of the Life-cycle of the Parasitic Nematode
    Strongyloides ratti

    Investigating Hookworm Genomes by Comparative Analysis of Two Ancylostoma
    Species

As of 11/15/2004, all databases have been updated.

• There are 127 EST libraries in NemaBLAST from 29 organisms. A new build of nemnoele has also been added.
• There is a total of 12 organisms clustered in NemaGene Cluster Search & NemaGene Cluster BLAST. Trichuris vuplis, Ascaris suum, & Haemonchus contortus recently added.
• Library descriptions are up to date.
• Accession IDs available for all ESTs.

New publications:

• A transcriptomic analysis of the phylum Nematoda.

In the News:

• Nematodes Trichinella spiralis and Pristionchus pacificus to move to full-genome scale sequencing

New publications:

• A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans.
• Genomic Filtering, an Approach to Discovering Novel Trends in Parasitology
• Gene discovery in the adenophorean nematode Trichinella spiralis: an analysis of transcription from three life cycle stages
• mRNA Sequences for Haemonchus contortus intestinal cathepsin B-like cysteine proteases display an extreme in abundance and diversity among mammalian parasitic nematodes

New publications:

• Nematode.net: A Tool for Navigating Sequences from Parasitic and Free-living Nematodes
• Comparative Genomics of Gene Expression in the Parasitic and Free-living Nematodes Strongyloides stercoralis and Caenorhabditis elegans