Table 1.
GOPHER parameters: The users may chose parameter settings that influence the design of probes and digests. In addition, approach-specific parameters can be chosen
| Probe parameters | |
| Probe length | Explanation: Length of probes. |
| Default: 120 bp | |
| Minimum GC content | Explanation: The minimum proportion of G and C nucleotides. |
| Default: 35% | |
| Maximum GC content | Explanation: The maximum proportion of G and C nucleotides. |
| Default: 65% | |
| Alignability | Explanation: Maximum mean 50mer alignability. |
| Default: 2 | |
| Digest parameters | |
| Margin size | Explanation: Width of the outermost ends of digests that will be tiled with probes. |
| Default: 250 bp | |
| Minimum digest size | Explanation: Smaller digests cannot be selected. |
| Default: 120 bp | |
| Minimum number of probes | Explanation: At least this number of probes have to be placed in each margin of a balanced digest. The total number of probes in both margins of unbalanced digest must be at least twice this value. |
| Default: 1 | |
| Allow unbalanced margins | Explanation: Digest with unequal numbers of probes in each margin are selected during viewpoint creation. |
| Default: False | |
| Simple parameters | |
| Allow patching | Explanation: Digests that are not well centered at the TSS will be patched during viewpoint creation. |
| Default: False | |
| Extended parameters | |
| Maximum distance upstream | Explanation: Extension of the viewpoint in upstream direction |
| Default: 5000 bp | |
| Maximum distance downstream | Explanation: Extension of the viewpoint in downstream direction. |
| Default: 1500 bp |