The user can semi-automatically or manually select a reduced number of sequences for analysis and can also restrict the columns, e.g. exons could be extracted from a genomic alignment and saved as a new alignment.
Where multiple targets within a database produced alignments with significant E-values, the single best-scoring alignment was saved.
We used the training sets to build training resources for the automatic word alignment and saved the test sets for later use as a gold standard for the automatic word alignment.
When a conformer is overlaid on a reference shape, and the computed shape Tanimoto is above the Transform-Tanimoto, the data required to reproduce that alignment are saved (Figure 4).
The alignment was saved as a Phylip file and the graphic was generated using Version 6.2 of CLC Sequence Viewer (www.clcbio.com).
The gene structure with the correctly identified splice regions is derived from the scaffold alignment and saved in a General Feature Format (gff) file.
The protein space can be visualized as a graph-like structure, where nodes represent proteins and a significant alignment is saved as an edge between two nodes.
The alignment was saved in NEXUS format for the phylogenetic analysis.
The alignment was saved as a PAUP file and used to generate a phylogenetic tree using PAUP 4.0b6.
The duplicated segments identified for each pairwise alignment are saved as an output file in MAF format.
