Surface proteins are hydrophobic and remain difficult to study thereby necessitating the use of TM topology prediction methods such as TMHMM (1) and Phobius (2). However, there exists a need for bioinformatic approaches to streamline batch processing of isoforms for comparing and visualizing topologies. To address this gap, we have developed an R package, SurfaltR. It pairs inputted isoforms, either known alternatively spliced or novel, with their APPRIS (3) annotated principal counterparts, predicts their TM topologies using TMHMM or Phobius, and generates a customizable graphical output. Further, SurfaltR facilitates the prioritization of biologically diverse isoform pairs through the incorporation of three different ranking metrics and through protein alignment functions.
If you use surfaltr in published research, please cite the Bioconductor R package and possibly a subsequent publication (will be updated later).
As surfaltr is hosted on Bioconductor, please follow installation instructions outlined here: https://bioconductor.org/packages/release/bioc/html/surfaltr.html
# Please refer to the vignette for detailed descriptions of installation, workflow, functions and troubleshooting.
1. Sonnhammer EL, von Heijne G, Krogh A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol. 1998;6:175–82.
2. Käll L, Krogh A, Sonnhammer ELL. A combined transmembrane topology and signal peptide prediction method. J Mol Biol. 2004 May 14;338(5):1027–36.
3. Rodriguez JM, Rodriguez-Rivas J, Di Domenico T, Vázquez J, Valencia A, Tress ML. APPRIS 2017: principal isoforms for multiple gene sets. Nucleic Acids Res. 2018 Jan 4;46(D1):D213–7.