In case of the varying alignment, penalizing gaps heavily might occur. Then the best scoring local alignment between the sequences will be one that optimizes the score between matches and mismatches, without any gaps.

In bioinformatics, sequence alignment is a way of arranging DNA, RNA, or protein sequences to identify regions of similarity. These similarities may be a result of functional, structural, or evolutionary relationships between the sequences. Topics include:  Protein Motifs and Domain Prediction, Motif and Domain Databases Using Regular Expressions, Motif and Domain Databases Using Statistical Models, Protein Family Databases, Global Sequence Alignment, Local Sequence Alignment, Motif Discovery in Unaligned Sequences, Dot Matrix Sequence Comparison, Dynamic Programming Algorithm for Sequence... Show more

In bioinformatics, sequence alignment is a way of arranging DNA, RNA, or protein sequences to identify regions of similarity. These similarities may be a result of functional, structural, or evolutionary relationships between the sequences.

Topics include:  Protein Motifs and Domain Prediction, Motif and Domain Databases Using Regular Expressions, Motif and Domain Databases Using Statistical Models, Protein Family Databases, Global Sequence Alignment, Local Sequence Alignment, Motif Discovery in Unaligned Sequences, Dot Matrix Sequence Comparison, Dynamic Programming Algorithm for Sequence Alignment, Use of Scoring Matrices and Gap Penalties in Sequence Alignments, Assessing the Significance of Sequence Alignments, & Bayesian Statistics.

Show less