rIPRscan

Welcome to the alpha-testing phase of riprscan, premiered at GLBIO 2023!

Interested in running detailed a combination of evolutionary and domain architecture analyses for your protein(s) of interest? Check out our recent web-app, MolEvolvR and associated preprint – where we do all of these for you, and more!

Fasta –> protein scan outputs

Users can submit a single/multifasta file (amino acid/protein sequences) to receive detailed protein scan analyses, including match to domain profiles, localization, signal, and disorder predictions. Learn more about IPRscan here.

library(rinterpro)
submit_ipr(path2seq = here("inst/extdata/ex-in-CAA75348.1.faa"),
           outfolder = here("inst/extdata"),
           email = "jravilab.msu@gmail.com")

Cleaning up your output data

Coming soon!

cleanup_iprout(inpath='path/to/iprout', outpath='path/to/iprcln')

ipr2domarch(inpath='path/to/iprcln', outpath='path/to/ipr_da')

cleanup_domarch(prot='path/to/ipr_da',
                old = "DomArch.orig", new = "DomArch",
                domains_keep, domains_rename,
                repeat2s=TRUE, remove_tails = FALSE,
                remove_empty=F,
                domains_ignore=NULL)

Visualizing your data

Coming soon!

ipr2viz(infile_ipr = 'path/to/iprout', infile_full = 'path/to/metadata',
        accessions = c(), analysis = c("Pfam", "Phobius", "Gene3D"),
        group_by = "Analysis", topn = 20,
        name = "Name", text_size = 10, query = 'All')

Questions/Feedback?