Table 1.
Summary of Functions
| Program | Actiona | Modeb | Results |
|---|---|---|---|
| Add Sequence | |||
| *FSD + FPC functions | Simulated digest | Confirm location of clone | |
| Add clones from other maps | |||
| Anchor contigs to chromosomes | |||
| *BSS | Marker→BES | Batch or interactive | Electronic markers |
| Marker→Sequence | Merge FPC contigs | ||
| BSS | GRC→BES | Batch | Place GRCs on the map to eludicate gene rich regions. |
| GRC→Sequence | Merge FPC contigs | ||
| Selecting MTPc | |||
| *BSS | Sequence→BES | Interactive | Manual selection |
| *BSS + pickMTP | WGS→BES | Batch | Automatic selection |
| Finishingc | |||
| BSS | Draft→Sequence | Interactive | Locate draft (WGS or BAC-based) sequence that overlaps clone in order to use the reads and close sequencing gaps |
| BSS | WGS→BES | Interactive or batch | Merge FPC contigs |
(FSD) FPC Simulated Digest, (BSS) Blast Some Sequence, (BES) BAC End Sequence, (GRC) Gene Rich Contig, (WGS) Whole Genome Shotgun.
a
The GRC, WGS, and Draft would all be treated as markers in BSS, i.e., use the BSS Marker→Sequence and Marker→BES. Sequence refers to BAC-based sequence.
b
Interactive mode allows the user to add one marker at a time after confirming the marker by the BSS report and sequence alignment. Batch mode adds all markers at once, based on a user specified filter.
c
A marker added for a BES or for draft sequence may not be of interest for the release version of the database, in which case, a copy of the FPC database can be made for the intermediate results.
*
Features discussed in Results and Methods.