Generalized affine gap costs for protein sequence alignment

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Statistical potentials for fold assessment (2002, unknown): “Each target sequence was aligned separately with each one of the 1637 known structures by use of the program ALIGN that implements local sequence alignment by dynamic programming (Altschul 1998).”
Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. (2001, background): “Typically, protein sequence alignment methods use a relatively high gap-opening penalty and a significantly lower gap-extension penalty; the reasoning behind this is that inserts/deletions affect protein structure and therefore are tolerated only to a limited extent, but once such a mutation is fixe”
Recent developments in the MAFFT multiple sequence alignment program (2008, background): “E-INS-i uses a local pairwise alignment with the generalized affine gap cost [71], in which the unalignable region is left unaligned at the pairwise alignment stage.”
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. (2001, methodology): “Altschul ( 51 ) has suggested permitting a gap to leave an arbitrary and in general different number of residues in both sequences unaligned; the cost of a gap involving x and y residues in the two sequences, where x ≤ y, would be a + b(y – x )+ cx. We implemented such generalized affine gap costs f”