Needleman-Wunsch

When no gap penalty is used then the Needleman-Wunsch alignment may contain a largt unrealistic number of gaps. The simplest type of gap penalty (other than not to have one) i to use a length-dependent scheme in which one assigns a fixed negative value for each insertio ... 

Many algorithms have been employed for sequence analysis. They can be used for either protein or nucleic add sequences, and many of these were not developed specifically for molecular biological use, but for linguistic applications. It is beyond the scope of this book to discuss these algorithms in any detail the essentials of two of the most important methods, FASTA and Needleman-Wunsch will serve as examples of how algorithms are structured. 

Needleman-Wunsch alignment is performed in three steps ... 

Figure 5.4 Walk-through example of Needleman-Wunsch alignment.

Algorithms. Although there are many mechanisms to search biodatabases, the most critical and extensively used is sequence similarity searching. Needleman-Wunsch, Smith-Waterman, FASTA, and BLAST represent the major similarity algorithms. They differ in algorithmic mechanism and computational speed, with Needleman-Wunsch being the most accurate but also the most computationally intense. At the time of its publication in 1970, it took days to return results. BLAST is the least accurate of... 

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