| "Text Maps" data type for mapping motifs/modules/sequences to general (non-numeric) values | |
| "File data server" which can use a local file as a data source | |
| Support for "Gene Ontology" data | |
| Better support for CAGE data and alternative start sites | |
| Hyperlinks to sequence databases such as Ensembl, Gene Cards, HUGO, UniProt, etc. | |
| Automatic retrieval of orthologous sequences | |
| Include a tool which can be used to create and edit configuration
files for external programs | |
| Support for performing motif/module discovery and scanning with Web Servers | |
| Support for external programs that use configuration files rather
than command line arguments to specify their
parameters | |
| Operations (or analyses) for clustering sequences and motifs (into Partitions) | |
| Word wrapping in the protocol editor | |
| Statistical tests for calculating p-values when comparing distributions | |
| Automatic 'liftover' of feature datasets from different genome builds | |
| Ruler anchored at start of sequence | |
| combine_regions with union, set subtraction or intersection | |