BLAST Server

This server is primarily intended for analyzing VSG sequences (most recently updated in May 2017), especially for large-scale BLAST analyses (maximum 16,000 sequences per file) that cannot be done on other servers. The BLASTable databases include sequences not yet included in a publication, although most are now in GenBank. If you use these unpublished sequences, I would appreciate an email or other acknowledgement.

The TREU 927 files include ONLY chromosomes 1-11 v5.2, with 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 the current official versions.

Files available to download

Right click to download files: all are in plain text with informative fasta headers (including the annotation 'MC' for sequences derived from purified minichromosomes of Lister 427, TREU 927 & EATRO 1125). Files were up-to-date in May 2017. The assembly and annotation of Lister 427 complete and partial VSGs is described in 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. All my additions to the repertoire of TREU 927 VSGs are now included in GenBank, together with all EATRO 1125 (aka, incorrectly, as 'the AnTat strain') complete and partial VSGs that are at least 250 AAs long. The Lister 427 and TREU 927 data come from Illumina short-read assemblies; the EATRO 1125 data are derived from Illumina and PacBio sequencing. The Lister 427 genome and many of its incomplete VSG genes will be superseded by the soon-to-be published PacBio genome from Nicolai Siegel's laboratory, so I am no longer including my 2010 Illumina contigs on this site. All files are in FASTA format. I am no longer providing concatenated VSG files for IGV or Bowtie.

  • PROTEIN

  • All 13,171 VSGs of all species from all sources

  • VSGs Lister 427. All 4,211 >149 AAs (2010 Illumina Assembly)

  • VSGs Lister 427. Unique 2,470 >249 AAs (2010 Illumina Assembly)

  • VSGs EATRO 1125. All 5,349 >149 AAs (2015 PacBio & Illumina Assemblies)

  • VSGs EATRO 1125. Unique 3,250 >249 AAs (2015 PacBio & Illumina Assemblies)

  • VSGs. 2,990 of all species not provided by me parsed from GenBank & TriTrypDB May 2017

  • VSGs TREU 927. 644 New >149 AAs in 2012 Illumina assembly by me

  • DNA

  • EATRO 1125 PacBio Contigs (unpublished genome)

  • All 13,069 VSG CDSs of all species from all sources

  • VSG CDSs Lister 427. All 4,211 >149 AAs (2010 Illumina Assembly)

  • VSG CDSs Lister 427. Unique 2,470 >249 AAs (2010 Illumina Assembly)

  • VSG CDSs & Flanks Lister 427. Unique 2,470 >249 AAs (2010 Illumina Assembly)

  • VSG CDSs EATRO 1125. All 5,349 >149 AAs (2015 PacBio & Illumina Assemblies)

  • VSG CDSs & Flanks EATRO 1125. All 5,349 >149 AAs (2015 PacBio & Illumina Assemblies)

  • VSG CDSs EATRO 1125. Unique 3,250 >249 AAs (2015 PacBio & Illumina Assemblies)

  • VSG CDSs. 2,889 of all species not provided by me parsed from GenBank & TriTrypDB May 2017

  • VSG CDSs TREU 927. 644 New >149 AAs in 2012 Illumina assembly by me

  • Click here to return to tryps.rockefeller.edu home page