Name Mode Size
..
Crb1.Rd 100644 1 kb
align_org_prts.Rd 100644 2 kb
align_prts.Rd 100644 1 kb
check_tmhmm_install.Rd 100644 1 kb
clean_data.Rd 100644 2 kb
ensembl_db_retrieval.Rd 100644 1 kb
format_ids.Rd 100644 1 kb
get_aas.Rd 100644 1 kb
get_pairs.Rd 100644 2 kb
get_phobius.Rd 100644 3 kb
get_prts.Rd 100644 1 kb
get_tmhmm.Rd 100644 2 kb
graph_from_aas.Rd 100644 2 kb
graph_from_ids.Rd 100644 2 kb
graph_prots.Rd 100644 2 kb
hpa_genes.Rd 100644 1 kb
hpa_mouse_genes.Rd 100644 1 kb
merge_trans.Rd 100644 1 kb
plot_isoforms.Rd 100644 2 kb
process_tmhmm.Rd 100644 1 kb
rank_prts.Rd 100644 1 kb
run_phobius.Rd 100644 2 kb
split_fasta.Rd 100644 1 kb
test_surfaltr.Rd 100644 1 kb
tmhmm_fix_path.Rd 100644 1 kb
README.md
# surfaltr 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. # Note: If you use surfaltr in published research, please cite the Bioconductor R package and possibly a subsequent publication (will be updated later). # Installation: 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. # References 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.