What are pairwise sequence comparisons?

The aligning or comparing of two sequences.

Why are they useful?

nt/nt or protein/protein

• Shows you how similar sequences are.
• Highlight regions of similarity/differences.
• Find best region of similarity.
• More exacting alignments than fasta/blast.
• Look for overlaps.

genomic/est or genomic/protein

• reveal coding regions
• reinforce gene predictive methods

How good is my Alignment?

• Sequence identity/similarity
• length of alignment
• quality score
• actual alignment