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
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