Align to folder

This method uses a single query sequence and performs a search with that query on sequences stored in a single or nested folders, and enables you to:

- perform an optimal alignment between two nucleic acid sequences using scoring matrices and taking gaps into account

- Find related sequences to your query on your hard drive.

- perform an optimal alignment between a protein query sequence and either a protein sequence or a nucleic acid sequence, using scoring matrices and taking gaps into account

- View the alignments of a group of related sequences with the query sequence in a multiple-alignment format.

- Retrieve any hits direct to the Desktop, or fetch individual hits from within multi sequence files.

To perform alignments, a sequence window must be the active window. A scoring matrix appropriate for the sequence must be open or available on the hard disk.

THE SCORING matrix pre-filter

MacVector uses a scoring matrix to pre-filter the sequences under consideration. The match and mismatch scores used in the scoring can be reassigned, or new scoring matrices can be created and edited.

When it finds a match, MacVector computes an initial score for the matching sequence. You have the choice of using this score as a ranking to reject sequences before alignment. Alternatively, you can perform an optimal alignment on each sequence that passes a cut-off score, introducing gaps and indels if required, and calculate an optimal score to use as the basis for acceptance or rejection.