This server is primarily intended for analyzing VSG sequences (most recently updated April 2016), especially for local large-scale BLAST analyses that cannot be done on other servers. There are also BLASTable databases of my yet-to-be-submitted to NCBI (GenBank) or for publication TREU927 & EATRO1125 genomic and minichromosome VSGs not previously in any database. If you use these unpublished sequences, I would appreciate an email or other acknowledgement. These unpublished sequences are NOT presently included in the 'VSGs_all' or 'VSGs_non-427' database files.
The TREU927 files include ONLY chromosomes 1-11 v5.2 and annotations available in April 2016. The data sets contain all 10,144 cds and 9,661 proteins. Go to the TrypDB, TriTrypDB or NCBI servers if you want official versions.
VSG Files for Downloading
Right click to download files: all are in plain text. Files were last updated 6th August 2014. Non-VSGs are now hopefully fully removed (these included some ESAGs that are VERY similar to VSGs) and now contain only the 2,584 VSG sequences longer than 149 AAs. Lister 427 VSGs are also available at NCBI (GenBank). The assembly and annotation of these VSGs is described Capturing the Variant Surface Glycoprotein repertoire (the VSGnome) of Trypanosoma brucei Lister 427. Cross GAM, Kim H-S & Wickstead B. 2014 Mol Biochem Parasitol 195: 59-73.
The files for creating databases for the bowtie mapping application also contain some control non-VSG genes and repeat sequences. The files of concatenated VSG CDSs in fasta format (.fas) with corresponding coordinate (.bed) files are intended for mapping reads using the IGV (Interactive Genome Viewer) from the Broad Institute. To use IGV you first need to use bowtie against the same concatenated files to map your reads.
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