PT  - JOURNAL ARTICLE
AU  - Daniel Kogan
AU  - Vijay Kumar Ulaganathan
TI  - TraPS-VarI: a python module for the identification of STAT3 modulating germline receptor variants
AID  - 10.1101/173047
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 173047
4099  - http://biorxiv.org/content/early/2017/08/07/173047.short
4100  - http://biorxiv.org/content/early/2017/08/07/173047.full
AB  - Motivation Human individuals differ because of variations in the DNA sequences of all the 46 chromosomes. Information on genetic variations altering the membrane-proximal binding sites for signal transducer of transcription 3 (STAT3) is valuable for understanding the genetic basis of cancer prognosis and disease progression (Ulaganathan et al, 2015). In this regard, non-synonymous coding region mutations resulting in the alteration of protein sequence in the juxtamembrane region of the type I membrane proteins are biologically and clinically relevant. The knowledge of such rare cell line- and individual-specific germline receptor variants is crucial for the investigation of cell-line specific biological mechanisms and genotype-centric therapeutic approaches.Results Here we present TraPS-VarI (Transmembrane Protein Sequence Variant Identifier), a python module to rapidly identify human germline receptor variants modulating STAT3 binding sites by using the genetic variation datasets in the variant call format 4.0. For the found protein variants the module also checks for the availability of associated therapeutic agents in the therapeutic target database and the drugbank records.Availability The Source code and binaries are freely available for download at https://gitlab.com/VJ-Ulaganathan/TraPS-VarI and the documentation can be found at http://traps-vari.readthedocs.io/.Contact ulaganat{at}biochem.mpg.de & ulaganat{at}icloud.comSupplementary information Supplementary data enclosed with the manuscript file.