Department of Bioinformatics and Computational Biology

Transvar

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TransVar
Overview
Description
URL http://bioinformatics.mdanderson.org/main/transvar
Development Information
Language Python
Current Version 1.0
License GPL
Status Active
Last Updated 2015/02/07
References
Citations Zhou W, Chen T, Chong Z, Rohrdanz MA, Melott JM, Wakefield C, Zeng J, Weinstein JN, Meric-Bernstam F, Mills GB, Chen K. TransVar: a multi-level variant annotator for precision genomics. Nature Methods. In Press.
Help and Support
Discussion Project Forum


Contents


Source

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  • Please click this link to download the Python source code and read detailed command line usage.

Introduction

TransVar is a reverse annotator for inferring genomic characterization(s) of mutations (e.g., chr3:178936091 G/A) from protein or cDNA annotation(s) (e.g., PIK3CA p.E545K or PIK3CA c.1633G>A). It is designed for resolving ambiguous mutation origins, arising from alternative splicing.

TransVar has the following features:

  • supports HGVS nomenclature
  • supports both left-alignment and right-alignment convention in reporting indels.
  • supports annotation of a region based on a transcript dependent characterization
  • supports single nucleotide variation (SNV), insertions and deletions (indels) and block substitutions
  • supports mutations at both coding region and intronic/UTR regions
  • supports transcript annotation from commonly-used databases such as Ensembl, NCBI RefSeq and GENCODE etc
  • supports UniProt protein id as transcript id
  • supports GRCh36, 37, 38
  • functionality of forward annotation.

Frequently Asked Questions

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Forward annotation is

  • What is ?