SCOTCH
Surface Complementarity Trace in Complex History
SCOTCH: Supplementary informations
Format for the multiple sequence alignments of protein A and B
- Both alignments should be in FASTA format
- The first sequence should the same as the sequence in the .pdb file (for both proteins)
- In A and B alignments, the sequences shoud be sorted in the same order, each sequence corresponding to a different specie (see example below)
| Alignment for protein A | Alignment for protein B |
|---|---|
|
>gi|pdb| K---------PIW--EQIGSSFIQHYYQL >gi|50067|Schizo. pombe MTAENATLLEPVLGKDEIGWMFVQEYYTY >gi|270639|Ustilago maydis NAATAANGVSPSSAASEVGWLFVTQYYTF >gi|633800|Dicty. discoideum MQSVD-----PQV--VGVGKQFVEHYYGI >gi|95914|Emer. nidulans M---------ADF--QSIAQQFVTFYYQT >gi|303755|Crypto. neoformans MASTQPPVAAPDQSKQDVGWQFVPQYYNF >gi|95910|Candida albicans MSV--------DF---AVATEFCNFYYNQ |
>gi|pdb| QVQFKLVLVGDGGTGKTTFVK >gi|191692|Schizo. pombe DYLFKLLLIGDSGVGKSCLLL >gi|268227|Ustilago maydis DYLFKLLLIGDSGVGKSCLLL >gi|140019|Dicty. discoideum DYLIKLLLIGDSGVGKSCLLL >gi|332095|Emer. nidulans ---FKLVLVGDGGTGKTTFVK >gi|302981|Crypto. neoformans DFLIKLLLIGDSGVGKSCLLL >gi|356247|Candida albicans DYLFKLLLIGDSGVGKSCLLL |
- For best performances, filter out highly redundant sequences (>90% sequence identity)
- Discard remote homologs (below 25% sequence identity from the pdb sequence)
- Alignments should have more than 20 sequences and no less than 10 sequences
Contributors
Version history
- May 15, 2008 : SCOTCH is publicly available.
