منابع مشابه
Contact-based sequence alignment.
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 ...
متن کاملSegment-based multiple sequence alignment
In this PhD thesis the segment-based approach for multiple sequence alignment, initially introduced by the DIALIGN program, is thorougly investigated and substiantially improved. The segment-based approach belongs to the class of local alignment methods and thus is very strong in finding locally conserved motifs, whereas global methods align the input sequences globally from the beginning to en...
متن کاملSegment-based multiple sequence alignment
MOTIVATION Many multiple sequence alignment tools have been developed in the past, progressing either in speed or alignment accuracy. Given the importance and wide-spread use of alignment tools, progress in both categories is a contribution to the community and has driven research in the field so far. RESULTS We introduce a graph-based extension to the consistency-based, progressive alignment...
متن کاملMultiple Sequence Alignment Multiple Sequence Alignment
An algorithm for progressive multiple alignment of sequences with insertions " , 1. Introduction The problem of sequence alignment is to find the patterns of sequence conservation and similarity between pairs or sets of given sequences. In biological contexts, similarity between biological sequences usually amounts to either functional or structural similarities or divergence from a common ance...
متن کاملProtein sequence-structure alignment based on site-alignment probabilities.
A protein sequence-structure alignment method for database searches is examined on how effectively this method together with a simple scoring function previously developed can identify compatibilities between sequences and structures of proteins. The scoring function consists of pairwise contact energies, repulsive packing potentials of residues for overly dense arrangement and short-range pote...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2004
ISSN: 1362-4962
DOI: 10.1093/nar/gkh566