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This section contains links to filarial genome data, and microarray design and bioinformatics files that are indispensable for analyzing genome, transcriptome, and proteome data. Edited 1-5-13.

Filarial Genomes Available

Acanthacheilonema viteae, Blaxter lab at nematodes.org
Dirofilaria immitisBlaxter lab at nematodes.org
Litomosides sigmodontisBlaxter lab at nematodes.org
Onchocerca ochengi atBlaxter lab at nematodes.org
Wolbachia - Dirofilaria immitisBlaxter lab at nematodes.org
Wolbachia - Onchocerca ochengiBlaxter lab at nematodes.org
 

Ongoing Filarial Genome Projects

 

B. malayi RNAseq summary table @ Nematode.net

Nematode.net summary table for B. malayi RNAseq data, all mapped to the most recent B. malayi genome assembly. To access click here, and for relevant literature click here
 

Filarial Worm Database at the Broad Institute

Message from Tom Nutman, NIAID:  In the middle of 2009, we proposed to take advantage of new sequencing technologies to launch genomic studies of three filarial parasites that together infect an estimated 153 million people.  We generated sequence coverage of single adult worms to characterize polymorphisms from W. bancrofti and O. volvulus, and we generated a draft assembly of Loa loa (from microfilarial genomic DNA) to study crucial phenotypic difference among these closely related filarial species.  In addition, we expected these data would allow us to define the extent of synteny and to characterize heterozygosity that could help us plan the more comprehensive studies of population genetics. 

These data were collected as part of a collaboration between the Laboratory of Parasitic Diseases, DIR, NIAID and the Broad Institute with funding provided, in large part, by the NIAID Division of Microbiology and Infectious Diseases funded Genome Sequencing Center at the Broad Institute.  In late May 2010, all of the data (with annotation) was made public and available at the NCBI,  and all of the information can be found starting at the Filarial Worm Database* at the Broad Institute home page:

http://www.broadinstitute.org/annotation/genome/filarial_worms/Info.html

Not only will you find information about the L. loa, W. bancrofti, and O. volvulus genomes, but you will also find links to the B. malayi and C. elegans genomes.  Furthermore, sequence data on the Wolbachia endosymbionts of W. bancrofti (wWb), O. volvulus (wOv) and B. malayi (wBm) are available as well.

 *Funded by the NIAID

 


 

Keeping molecular nomenclature straight

Getting confused between EST names, gene identifiers, and genbank ID's?  Here is a complete guide to filarial molecular nomenclature.
 

B. malayi 2007 genome and microarray data

Brugia malayi coding sequences:  Click to download coding sequences from B. malayi genome (Bm1 nomenclature), FASTA format, from B. malayi genome assembly (Ghedin et al. 2007)

 

B. malayi peptide models:  Click to download predicted peptide sequences from B. malayi genome (XXXXX.m00YY nomenclature), FASTA format (Ghedin et al. 2007)

 

The B. malayi Gene Index:  Click to download consensus sequence and annotation data for B. malayi ESTs (TC nomenclature), text format (Quackenbush et al. 2000)

 

B. malayi microarray version 2:  Click here for Gene models used for oligo design (BMW nomenclature), FASTA format.


B. malayi microarray version 2: Click here for Excel sheet correlating oligo name, model name, oligo source, and annotation for BLAST matches


B. malayi microarray version 2:  Click here for Excel sheet correlating oligo name, sequence, model name, oligo source, annotation by BLAST, Brugia model name. Multiple sheets feature changes to workbook, Wolbachia model oligos, B. malayi model oligos, and B. malayi proteome data.

 

B. malayi 2009 Microarray Annotation

From Li et al. 2009 (PMID:PMC2708187), supplemental files include most recent summaries of BmV2array BLAST outputs, C. elegans RNAi correlations, protein domain matches, KEGG analysis.

 

 Want to query or browse filarial gene expression datasets?  

Try NCBI, NCBI GEO (Gene Expression Omnibus), Spidey, NEMBASE3, nematode.net, Wormbase, and EMBL ArrayExpress.

 

Want to perform in silico subtraction of filarial ESTs?

The Brugla malayi Gene Index allows you to search B. malayi cDNA libraries by keyword, library identifier, and by library specific assemblies.  This type of query allows you to search for EST clusters that are expressed exclusively or predominantly in specific libraries, and is basically a way to perform 'electronic subtraction' of life cycle stage cDNAs.  This capability is also present at NEMBASE3.

 

 

 

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