P

protein sequence analysis

Small C programs I wrote for the paper "Le Novère N., Corringer P.J. and Changeux J.P. Improved secondary structure predictions for a nicotinic receptor subunit.Incorporation of solvent accessibility and experimental data into a 2D representation. Biophysical Journal (1999), 76: 2329-2345."

DPCfam Workstation version. Runs on Linux-based systems. Developed and tested on Ubuntu 18. DPCfamW uses the moodycamel::ConcurrentQueue library ( https://github.com/cameron314/concurrentqueue ) freely available provided citation (Simplified BSD license). This version replicates the pipeline used in to anlayze UniRef50 (v. 2017_07) as in Unsupervised protein family classification by Density Peak clustering, Russo ET, 2020, PhD Thesis ( http://hdl.handle.net/20.500.11767/116345 ), but with smaller datasets. Largest dataset we analysed is the TESTproteins_cd50.fasta datased we provide in this package. Due to memory bounds we do not guarantee that the abalysis of largest datasets is acheivable with this version.

This repository contiains the implementation of DPC-based algorithm as described in Russo, E.T., Laio, A. & Punta, M. Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation. BMC Bioinformatics 22, 121 (2021). https://doi.org/10.1186/s12859-021-04013-x. Note that the implementation has been written with the puropose of analysing, on a traditional workstation (8GB ram, 4-8 cores), query datasets with up to 5000 proteins, as those analysed in the reference paper.