A survey of sequence alignment
نویسنده
چکیده
We give a general overview of different perspectives on the meaning and creation of sequence alignments. Our points of view come from statistical, computational, algorithmic, evolutionary, and biological directions. We then survey recent work on algorithms in this area, focusing on local pairwise alignment of DNA sequences, but also discussing some recent work on multiple and global alignments.
منابع مشابه
An Application of the ABS LX Algorithm to Multiple Sequence Alignment
We present an application of ABS algorithms for multiple sequence alignment (MSA). The Markov decision process (MDP) based model leads to a linear programming problem (LPP), whose solution is linked to a suggested alignment. The important features of our work include the facility of alignment of multiple sequences simultaneously and no limit for the length of the sequences. Our goal here is to ...
متن کاملgpALIGNER: A Fast Algorithm for Global Pairwise Alignment of DNA Sequences
Bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity. Many computational algorithms have been applied for solving the sequence alignment problem. Dynamic programming, statistical methods, approximation and heuristic algorithms are the most common methods appli...
متن کاملGenetic variations of avian Pasteurella multocida as demonstrated by 16S-23S rRNA gene sequences comparison
Pasteurella multocida is known as an important heterogenic bacterial agent causes some severe diseases such as fowl cholera in poultry and haemorrhagic septicaemia in cattle and buffalo. A polymerase chain reaction (PCR) assay was developed using primers derived from conserved part of 16S-23S rRNA gene. The PCR amplified a fragment size of 0.7 kb using DNA from nine avian P. multocida isolates...
متن کاملA generalization of Profile Hidden Markov Model (PHMM) using one-by-one dependency between sequences
The Profile Hidden Markov Model (PHMM) can be poor at capturing dependency between observations because of the statistical assumptions it makes. To overcome this limitation, the dependency between residues in a multiple sequence alignment (MSA) which is the representative of a PHMM can be combined with the PHMM. Based on the fact that sequences appearing in the final MSA are written based on th...
متن کاملIT - Business Strategic Alignment and Organizational Agility: The Moderating Role of Environmental Uncertainty
This study investigates the effect of IT-business strategic alignment on organizational agility by considering the effects of IT flexibility and IT capability on strategic alignment. Also this study investigates the moderating role of environmental uncertainty on the relationship between strategic alignment and organizational agility. This research is an applied research based on purpose and de...
متن کامل