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dosorio / Peptides

An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.
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Can this package support analysing more than one peptide concurrently? #51

Open Mycorrhiza94 opened 2 years ago

Mycorrhiza94 commented 2 years ago

Thank you Dosorio for the useful package.

Within the existing package in R, is there a way to possibly input a text.file of peptide sequences (perhaps FASTA format) which can be analysed and a file outputted with the peptide analysis result as well as the run parameters and/or scales implemented for said run?

Would be great to take advantage of the mass analysis of peptides with the peptides package.

PhD Student (University of Nottingham)

dosorio commented 2 years ago

Hi @Mycorrhiza94, the functions are designed to take vectors of protein sequences at once, for each sequence a metric is returned. Please let me know if you have other questions. Best wishes, Daniel

avl911 commented 1 year ago

Hi Daniel! I just wonder if could be possible to cycle through a for loop over all my peptides sequences, in order to analyze more than one sequence at once? I mean, like an attempt to answer what @Mycorrhiza94 asked and analyze multiple entries contained in a fasta file. Thanks in advance

Abraham

jspaezp commented 1 year ago

Hey there!

I think most functions are vectorized, so if you make a character vector with your peptide sequences you would be able to analyze all of them at the same time.

> library(Peptides)
> mypeps <- c("MYPEPTIDE", "MYPINKPEPTIDE")
> hydrophobicity(mypeps)
[1] -1.033333 -1.061538

LMK if that helps of feel free to let us know what the friction point is for you. Best, Sebastian