Filarial Genomics and Bioinformatics

This section contains microarray design and bioinformatics files that are indispensable for analyzing genome, transcriptome, and proteome data. We recommend that you start with the 'Nomenclature Tracking' file to familiarize yourself with nomenclature.

Nomenclature Tracking: What does a name mean? Use this guide to decode 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.

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