JavaStudioTM Design for BlastView_align

BlastView_align provides the alignment services of BlastView, relying on two subcomponents that are also composite components, BlastView_inferred and BlastView_clustal. When the user first chooses to align a set of sequences in BlastView from the SequenceList component, the sequences are passed to BV_inferred for an "inferred" alignment. This is a multiple sequence alignment constructed solely based on the pairwise alignments of the selected sequences to the original query sequence. It is very fast to construct, because the necessary computation has already been performed by BLAST. From the inferred alignment window, the user may choose to invoke a ClustalW alignment process. This is run on a remote server and is managed by BlastView_clustal.