Developed by Vamsee Reddy

What is BioV?

     BioV is a collection of novel python tools designed to aid researchers in the field of transport protein evolution. BioV scripts integrate seamlessly with the Transport Classification Database (TCDB), allowing researches to work directly with individual TC-systems or entire families/superfamilies. BioV tools operate as standalone scripts or as python wrappers to accomodate both researchers and developers.

Who is using BioV?

     The BioV toolkit is the current laboratory standard used at the UCSD Saier Lab. We are the founders of the most complete and well known IUBMB approved Transport Classication Database (TCDB.org). We have produced over 700 publications from our lab.
  • Saier MH Jr, Yen MR, Noto K, Tamang DG, Elkan C. (2009), The Transporter Classification Database: recent advances,
    Nucl. Acids Res., 37: D274-8. [19022853]
  • Saier MH Jr, Tran CV, Barabote RD. (2006), TCDB: the Transporter Classification Database for membrane transport protein
    analyses and information, Nucl. Acids Res., 34: D181-6. [16381841]

     Over the years we have refined our techniques repeatedly and have assembled our most useful in-house designed tools for public use.

Some research aided by BioV

  • Discovery of the historic 2 TMS precursor in the Major Facilitator Superfamily. (V. S. Reddy, M. Shlykov, and M. Saier, 2012)
  • Novel discovery of the Junctional superfamily, interrelating Connexins, Innexinx,
          Claudins & Occludins. (V.S. Reddy and M. Saier. 2012)
  • 2011 topological analysis of current transporter families with TMStats (V.S. Reddy, and M. Saier, 2012)
  • Analysis of the Tetrahymena genome using BioV's GBlast. (U. Kumar & V.S. Reddy, 2012)
  • Common ancestry of the APC and MFS superfamily (V.S. Reddy, and M. Saier, 2012)
  • Data generated by the BioV Suite resulted in funding for Transporter PDB.

How to get BioV

BioV is readily available to download free of charge. BioV has several dependancies. They are as follows:
1 ) EMBOSS Package
2) Python 2.7
3) Matplotlib
4) HMMTOP
5) BioPython
6) Pearson's FASTA Tools
7) Mechanize

Once all the dependancies are installed, you may download the latest release of BioV here

Extensive documentation on all BioV Suite programs can be found here

The BioV Suite was developed by Vamsee Reddy at the UCSD Saier Lab.