Identifying distantly related protein sequences

Identifying distantly related protein sequences

The most powerful method available today for inferring the biological function of a gene (or the protein that it encodes) from its sequence is similarity searching on protein and DNA sequence databases. With the development of rapid methods for sequence comparison, both with heuristic algorithms and powerful parallel computers, discoveries based solely on sequence homology have become routine. ...

INTERALIGN: interactive alignment editor for distantly related protein sequences

SUMMARY Improving and ascertaining the quality of a multiple sequence alignment is a very challenging step in protein sequence analysis. This is particularly the case when dealing with sequences in the 'twilight zone', i.e. sharing < 30% identity. Here we describe INTERALIGN, a dedicated user-friendly alignment editor including a view of secondary structures and a synchronized display of carbon...

Revisiting amino acid substitution matrices for identifying distantly related proteins

MOTIVATION Although many amino acid substitution matrices have been developed, it has not been well understood which is the best for similarity searches, especially for remote homology detection. Therefore, we collected information related to existing matrices, condensed it and derived a novel matrix that can detect more remote homology than ever. RESULTS Using principal component analysis wi...

Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences.

Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more experimentally solved structures are available as templates for protein structure modeling. Toward this end, recent structure prediction methods...

Identifying and Quantifying Orphan Protein Sequences