Final answer:
To align more than two sequences using an approach similar to Needleman-Wunsch, one would use multiple sequence alignment tools like ClustalW or T-Coffee, which handle simultaneous alignments and provide iterative refinements for accuracy. Scoring functions and E-values help determine the quality of an alignment.
Step-by-step explanation:
Aligning more than two sequences with the Needleman-Wunsch algorithm, a method for performing global sequence alignment, can be computationally intensive, particularly with the large amount of data in repositories such as GenBank.
To address this, sequences might be broken into shorter segments, or words, for a simultaneous comparison which is a technique similar to the one used by the BLAST algorithm.
However, to perform a multiple sequence alignment specifically with the Needleman-Wunsch algorithm, specialized software or adapted algorithms designed for multiple sequence alignment, such as ClustalW or T-Coffee, would be needed.
These tools adjust the original pairwise approach of the Needleman-Wunsch to handle multiple sequences at once and often include additional features such as iterative refinement, which helps in improving the alignment accuracy.
Scoring functions and penalties for gaps (inserting spaces into the sequence alignment) play a key role in determining the optimal alignment.
Extension of an alignment or introduction of gaps is typically scored with respect to a predefined scoring system that considers both the match/mismatch of nucleotides and the evolutionary implications of insertions or deletions.
The Expected value or E-value assists in distinguishing between alignments that represent significant similarities and those which might have occurred by random chance.