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Comparative genomics : nematode protein families

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[Sept.15.2015]   
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NemFam - A database of conserved, nematode-derived protein families

NemFam (Nematode-derived protein Families) is a collection of nematode related, conserved regions of proteins that were not (when originally built) represented in Pfam. Over 214,000 polypeptides from 32 nematode species (27 of which are parasites of vertebrates or plants) were grouped into families using a clustering method that relies on the Markov Cluster Algorithm (MCL). Families were then multiply aligned, and those families having at least 10% of their full alignment length represented by at least 3 overlapping nematode species became candidate members of NemFam. These candidates were then screened against Pfam, and those with no members hitting Pfam were assembled into the final NemFam set.

How to make use of this resource

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.

Publication Link

Molecular determinants archetypical to the phylum Nematoda, Yin Y, Martin J, Abubucker S, Wang Z, Wyrwicz L, Rychlewski L, McCarter JP, Wilson RK, Mitreva M. BMC Genomics. 2009 Mar 18;10:114.


Jump to NemFam family page:
Enter either a NemFam id (such as NF_0307_0315), an EST contig name (such as MI04602), or an EST name (such as ra85g01.y1) to jump directly to a specific family. Or click the Advanced search link for more options.
NemFam id:
EST contig name:
EST name:

 

Conserved Nematode families from full-length genes

Proteins from four nematode species - Brugia malayi, Meloidogyne incognita, Meloidogyne hapla and Trichinella spiralis - were clustered using the OrthoMCL algorithm to build orthologous families, along with two outgroups, Drosophila melanogaster and Saccharomyces cerevisiae. From these families, 2517 groups were conserved in nematodes and 274 were found only in the nematodes, out of which 85 groups were single-copy genes.

Publication Link : The draft genome of the parasitic nematode Trichinella spiralis, Makedonka Mitreva,Douglas P Jasmer,Dante S Zarlenga,Zhengyuan Wang,Sahar Abubucker,John Martin,Christina M Taylor,Yong Yin,Lucinda Fulton,Pat Minx,Shiaw-Pyng Yang,Wesley C Warren,Robert S Fulton,Veena Bhonagiri,Xu Zhang,Kym Hallsworth-Pepin,Sandra W Clifton,James P McCarter,Judith Appleton,Elaine R Mardis & Richard K Wilson Nature Genetics 43,225-235 (2011).


 
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