• Corpus ID: 14683398

An Efficient Progressive Alignment Algorithm for Multiple Sequence Alignment

  title={An Efficient Progressive Alignment Algorithm for Multiple Sequence Alignment},
  author={Allam Appa Rao and Gumpeny Ramachandra Sridhar},
Summary Analyzing and comparing the string representations of sequences reveals a lot of useful information about the sequences. As new biological sequences are being generated at exponential rates, sequence comparison is becoming increasingly important to draw functional and evolutionary inference of proteins. This paper presents a partitioning approach for biomolecular sequence alignment that significantly improves the solution time and quality of the problem. The algorithm solves the… 

Figures from this paper


This research performs alignment of DNA sequences coding of cellulase to look for potential primer in order to increase the productivity of cellulases enzymes by Multiple Sequence Alignment (MSA) method.



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

A survey of multiple sequence comparison methods.

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.

A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins

A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed. From these findings it is possible to determine whether significant homology

Comparison of methods for searching protein sequence databases

  • W. Pearson
  • Computer Science
    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.

Identification of common molecular subsequences.

An Algorithm for the Distance Between Two Finite Sequences

  • P. Sellers
  • Computer Science
    J. Comb. Theory, Ser. A
  • 1974

A survey of multiple sequence comparison methods

Multiple sequence comparison refers to the search for similarity in three or more sequences. This article presents a survey of the exhaustive (optimal) and heuristic (possibly sub-optimal) methods