High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH

Background: Protein alignments are an essential tool for many bioinformatics analyses. While sequence alignments are accurate for proteins of high sequence similarity, they become unreliable as they approach the so-called 'twilight zone' where sequence similarity gets indistinguishable from random. For such distant pairs, structure alignment is of much better quality. Nevertheless, sequence alignment is the only choice in the majority of cases where structural data is not available. This situation demands development of methods that extend the applicability of accurate sequence alignment to distantly related proteins. Results: We develop a sequence alignment method that combines the prediction of a structural profile based on the protein's sequence with the alignment of that profile using our recently published alignment tool SABERTOOTH. In particular, we predict the contact vector of protein structures using an artificial neural network based on positionspecific scorin...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Florian Teichert, Jonas Minning, Ugo Bastolla, Markus Porto
• Keywords: BMCBI 2010, Proteins, Sequence Alignments, Sequence Similarity