bioLegato - Selecting Data

bioLegato Online Help

Grouping sequences

BioLegato provides the ability to specify sets of sequences as groups. If an operation is performed on one sequence, it will be performed on all members of the group simultaneously. Some examples in which grouping is useful include:

insertion or deletion of gaps or columns from a multiple alignment
exporting a specific set of sequences to a file
performing multiple alignment or phylogenetic analysis on a specific set of sequences
copying a set of sequences to a new bioLegato window
deleting a specific set of sequences from analysis
protecting a specific set of sequences from accidental modification

To create a group:

1. Select the sequences using any combination of selection methods to highlight all sequence names to be in the group (eg. click in sequence names, use Edit --> Select sequence by name).

2. Choose Edit --> Group.

If a number appears in the leftmost column of the name pane, it indicates the group of which a sequence is a member. Sequences that are not a member of any group are denoted by an underscore character.

In the example above, two groups have been defined. Group 1 comprises sequences only from leguminous plants, such as pea, bean and chickpea. Group 2 comprises sequence only from cucumber. Only Group 2 sequences are highlighted, so subsequent operations would only affect Group 2 sequences.

Membership in a group does not prevent you from working individually with each member of the group. Click once on a sequence name to select that sequence. Click once to choose an individual sequence, or double-click to choose the entire group.

One exception is that when a group exists, insertion and deletion operations will work on all members of the group. We need to sort out, in a future release, a more flexible approach.

Notes:

1. Currently, bioLegato does not have an implicit mechanism for iterating execution of a program for all members of a group. For example, if Group 2 was selected as shown above, you might expect bioLegato to run a program like BACHREST three times, once for each member of the group, and produce three restriction site search reports. However, BACHREST expects to read a file containing only a single sequence. An error would be generated if more than one sequence were present. At present, bioLegato just assumes you know what you're doing. A future version of bioLegato should be able to iterate program execution when more than one sequence is selected.
2. The current implementation of bioLegato has a rather limited group capability. A future version will implement groups as formal sets, allowing all common set operations, such as AND, OR, adding and deleting members etc.

To ungroup sequences:

1. Select the group. This can be done either by double-clicking on any member of the group, or selecting a member of the group, and then choosing Edit --> Select group.

2. Edit --> Ungroup.