Pairwise Sequence Alignment

  title={Pairwise Sequence Alignment},
  author={David WheelerVersion},
Only alignment of homologous sequences seems meaningful as it is unclear what an alignment of non-homologous sequences means. So as viewed here, an alignment is a partial reconstruction of the path of molecular evolution. Solving ii. above is highly motivating for a molecular biologist. The moment a new molecule A is found to be homologous to an old well studied molecule B, much of the knowledge of B probably is true for A as well. This is because function and structure evolves much slower than… 
FPGA architecture for pairwise statistical significance estimation
This work develops algorithms for sequence-specific strategies for hardware acceleration of pairwise sequence alignment in conjunction with statistical significance estimation, and provides a 'flexible array' hardware architecture which provides a scalable systolic array suitable for both long and short sequences.
Faster Sequence Alignment using Suffix Tree and Data-Mining Techniques
This thesis presents an application of a generalized suffix tree extended by the use of frequency of patterns, to perform accurate and faster biological sequence analysis as an improvement on the
Computational analysis and characterization of alternative splicing and its impact on transcriptional diversity
In all eukaryotes, pre-mRNA splicing is a requirement for protein synthesis as most coding sequences are interspersed with non-coding ones that need to be removed from the primary transcript. The
Empirical evaluation of methods for de novo genome assembly
A thorough comparison of the de novo assembly algorithms is made to allow new users to clearly understand the assembly algorithms: overlap-layout-consensus and de-Bruijn-graph, string-graph based assembly, and hybrid approach.
A short note on dynamic programming in a band
  • J. Gibrat
  • Computer Science, Medicine
    BMC Bioinformatics
  • 2018
It is suggested that dynamic programming in a band is well suited to the problem of aligning long reads between themselves and can be used as a core component of methods for obtaining a consensus sequence from the long reads alone.
Incorporating genomics into the toolkit of nematology.
The current state of nematode genomics is reviewed and some of the highlights that these genomes have revealed and the trend and benefits of ecological genomics are discussed, emphasizing the potential for new genomes and the exciting opportunities this provides for nematological studies.
ADAPTABLE: a comprehensive web platform of antimicrobial peptides tailored to the user’s research
The concept of “property alignment” to create families of property and sequence-related peptides (SR families) is introduced, which provides the researcher with a tool to select those AMPs meaningful to their research from among more than 40,000 nonredundant sequences.
Semi-local String Comparison: Algorithmic Techniques and Applications
  • A. Tiskin
  • Mathematics, Computer Science
    Math. Comput. Sci.
  • 2008
It is concluded that semi-local string comparison turns out to be a useful algorithmic plug-in, which unifies, and often improves on, a number of previous approaches to various substring- and subsequence-related problems.
Using event sequence alignment to automatically segment web users for prediction and recommendation
This thesis presents a novel methodological point of view in the area of sequence alignment in web usage mining, including user clustering and web prediction and recommendation, and shows applicable approaches in the quest to improve previous related work.
The emerging era of “new biology” accompanied by the birth of other branches of sciences, such as bioinformatics and computational biology, which have an integrated interface of molecular biology.


Progressive sequence alignment as a prerequisitetto correct phylogenetic trees
SummaryA progressive alignment method is described that utilizes the Needleman and Wunsch pairwise alignment algorithm iteratively to achieve the multiple alignment of a set of protein sequences and
Basic local alignment search tool.
Comparative biosequence metrics
The sequence alignment algorithms of Needleman and Wunsch (1970) and Sellers (1974) are compared and the two procedures are proven to be equivalent.
Rapid similarity searches of nucleic acid and protein data banks.
  • W. Wilbur, D. Lipman
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 1983
An algorithm for the global comparison of sequences based on matching k-tuples of sequence elements for a fixed k results in substantial reduction in the time required to search a data bank when compared with prior techniques of similarity analysis, with minimal loss in sensitivity.
Comparison of methods for searching protein sequence databases
  • W. Pearson
  • Mathematics, Medicine
    Protein science : a publication of the Protein Society
  • 1995
Search sensitivity with either the Smith‐Waterman algorithm or FASTA is significantly improved by using modern scoring matrices, such as BLOSUM45–55, and optimized gap penalties instead of the conventional PAM250 matrix.
An Overview of Sequence Comparison Algorithms in Molecular Biology
A review of the now classic and most established technique: dynamic programming and a number of interesting variations of this basic problem are examined that are specifically motivated by applications in molecular biology.
Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology
A method is presented that is asserted to provide all hypothetical ancestral character states that are consistent with describing the descent of the present-day character states in a minimum number of changes of state using a predetermined phylogenetic relationship among the taxa represented.
Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology
The author examines the importance of (sub)sequence comparison in molecular biology, core string edits, alignments and dynamic programming, and a deeper look at classical methods for exact string matching.
Algorithms for Approximate String Matching
  • E. Ukkonen
  • Computer Science, Mathematics
    Inf. Control.
  • 1985
An improved algorithm that works in time and in space O and algorithms that can be used in conjunction with extended edit operation sets, including, for example, transposition of adjacent characters.