ABSTRACT
In earlier chapters you viewed pairwise sequence alignments generated by BLAST. The various versions of BLAST (for example, BLASTN or BLASTP) aligned the query to the subject and you were able to see the individual differences between the two sequences. But if you had multiple hits to many paralogs, for example, it was difficult to identify sequence held in common between all the sequences without scrolling the browser window up and down to look at the alignment details. In this chapter, through the use of multiple sequence alignments, you will be able to easily see the relationships between sequences: their similarities, highly conserved regions, hotspots for change, and the relationships between isoforms.
