We present a profile-profile multiple alignment strategy that uses database searching to collect homologues for each sequence in a given set, in order to enrich their available evolutionary information for the alignment. For each of the alignment sequences, the putative homologous sequences that score above a pre-defined threshold are incorporated into a position-specific pre-alignment profile....

As with pairwise alignment, multiple sequence alignments (MSAs) are typically scored by assigning a score to each column and summing over the columns. The most common approach to scoring individual columns in a multiple alignment is to calculate a score for each pair of symbols in the column, and then sum over the pair scores. This is called sum-of-pairs or SP-scoring. For global multiple seque...

The need to measure sequence similarity arises in information extraction, music mining, biological sequence analysis, and other domains, and often coincides with sequence alignment: the more similar two sequences are, the better they can be aligned. Aligning sequences not only shows how similar sequences are, it also shows where there are differences and correspondences between the sequences. T...

Current DNA sequencing methods can accurately determine only a few hundred ‘letters’ (bases) off each end of a contiguous stretch of DNA. It is therefore impossible to read a complete genome all at once. The human genome, for example, consists of about 3 billion base pairs — in contrast to about 500 that can be read at a time. The Whole Genome Shotgun Sequencing Method addresses this problem by...

Sequence alignment is one of the most fundamental problems in computational biology. Ordinarily, the problem aims to align symbols of given sequences in a way to optimize similarity score. This score is computed using a given scoring matrix that assigns a score to every pair of symbols in an alignment. The expectation is that scoring matrices perform well for alignments of all sequences. Howeve...

This paper introduces the novel method of contact-based protein sequence alignment, where structural information in the form of contact mutation probabilities is incorporated into an alignment routine using contact-mutation matrices (CAO: Contact Accepted mutatiOn). The contact-based alignment routine optimizes the score of matched contacts, which involves four (two per contact) instead of two ...

With the goal of developing e cient multiple structural alignment methods, we have asked which of the pairwise structure alignment methods lends itself most readily to generalization to multiple structure alignment. A simple linear encoding of the sequence and associated residue conformation can be treated by standard multiple sequence alignment methods.

The sequence alignment is a fundamental problem in computational biology. Many sequence alignment methods have been proposed, such as pair-wise sequence alignment, multiple sequence alignment (MSA), syntenic alignment, constraint multiple sequence alignment, and etc. Among them, pair-wise sequence alignment is a most commonly used method. Recently, MSA is more and more important which has been ...

This paper presents an approach for establishing correspondences in time and in space between two different video sequences of the same dynamic scene, recorded by stationary uncalibrated video cameras. The method simultaneously estimates both spatial alignment as well as temporal synchronization (temporal alignment) between the two sequences, using all available spatio-temporal information. Tem...