Updated
Nov 14 08
Anabelle stuff 
Notes
Nov 14 08
ann GFF examples on all lines
GN numbering handling…
Nov 13 08
- rule with Chop + FT annotation in the chopped region
- Chop and Size: size before chop
- Related ! : overlap or inclusion?
- Topology ! : not implemented?
- Fusion: implemented?
- Duplicate
- Plasmid
- samann.pl GN preprocessing
- minimal annotation GFF!
Nov 13 08
| method | name | prog |
| ps_scan | [PSxxxxx] | ps_scan.pl v1.67 |
| repeat | Repeat_x..x | repeater.perl v3.4 |
| InterPro | [motifAC] | use ip db |
| eskw | Transmembrane | eskw.pm reimplemented in perl |
| TMHMM | Transmembrane | tmhmm v2.0 |
| memsat | Transmembrane | Copyright© 1993 David T. Jones |
| Phobius | Transmembrane/Signal | phobius.pl v1.00 |
| BLAST | [entryAC] | blastall.remote (SIB BLAST network client v1.3) |
| coils | Coiled_coil | coils2 v1.2 |
| GPI | GPI_anchor | http://mendel.imp.ac.at/gpi/cgi-bin/gpi_pred.cgi&&http://mendel.imp.ac.at/gpi/cgi-bin/gpi_pred_plants.cgi&&http://mendel.imp.ac.at/gpi/cgi-bin/gpi_pred_fungi.cgi |
| NMT | Myristate | http://mendel.imp.ac.at/myristate/cgi-bin/myr_pred.cgi |
| NMT_NN | Myristate | myristo_listefichier ! |
| polyaa | POLY_xxx | polyaa.pm regexp… |
| ext_sulfinator | Sulfation | http://www.expasy.org/cgi-bin/sulfinator.pl |
| SignalP | Signal | signalp 3.0a |
| TargetP | Signal | targetp v1.1 |
| netNglyc | N_glycosylation | netNglyc v1.0a |
| NetOglyc | O_glycosylation | netOglyc v3.1b |
trigger=yes in hamap
| Coiled_coil | 15 |
| PF… | 6 |
| PS… | 208 |
| Signal | 42 |
| Transmembrane | 161 |
fields
| feature name | seq_ac | prog | start | stop | score | conf_level | local_alignment |
| Transmembrane | Y | Y | Y | Y | Y | y | - |
| Signal | Y | Y | Y | Y | Y | y | - |
| N/O_glycosylation | Y | Y | Y | Y | y | y | ~ |
| Myristate | Y | Y | Y | Y | y | y | - |
| Sulfation | Y | Y | Y | Y | y | y | - |
| POLY_xxx | Y | Y | Y | Y | - | - | - |
| GPI_anchor | Y | Y | Y | Y | Y | y | - |
| Sulfation | Y | Y | Y | Y | Y | - | - |
| PSxxxx | Y | Y | Y | Y | Y | y | y |
| Repeat_x..x | Y | Y | Y | Y | Y | y | - |
note: for onion, modules will have to be created to parse each of the prog output! ... level is sometimes deduced based on score!... most of the prog give start stop score etc… could be loaded in a generic table…
note: maybe onion could use anabelle sequence analysis module (for some methods), as is…