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Aligning protein sequences using a score matrix has became a routine but valuable method in modern biological research. However, alignment in "Twilight Zone" is still a challenging issue. New score matrices such as Position Specific Score Matrix and structural context-based matrix have been issued to deal with it, whereas generalized matrices are still useful in pairwise alignment and/or...
Sequence alignment has been a most commonly used method in modern biological research. However, sequence alignment in "Twilight Zone" is still a challenging issue. Three protein class-specific matrices are constructed to investigate whether alignment in "Twilight Zone" can be improved by using class-specific matrices and gap penalties. The substitution pattern differences between...
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