Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation.

ABSTRACT:

Background

The identification of protein families is of outstanding practical importance for in silico protein annotation and is at the basis of several bioinformatic resources. Pfam is possibly the most well known protein family database, built in many years of work by domain experts with extensive use of manual curation. This approach is generally very accurate, but it is quite time consuming and it may suffer from a bias generated from the hand-curation itself, which is often guided by the available experimental evidence.

Results

We introduce a procedure that aims to identify automatically putative protein families. The procedure is based on Density Peak Clustering and uses as input only local pairwise alignments between protein sequences. In the experiment we present her

SUBMITTER: Russo ET 

PROVIDER: S-EPMC7955657 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature