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Monday, February 17th 2003 : NPS@ release 3.0 is now running on a Linux cluster
HMMER (hmmbuild and hmmsearch) is now available (see news)
Job CLUSTALW (ID: 3052) is running on NPS@ server (started on Mon Aug 4 02:18:26 CEST 2003).
Results will be shown below. Please wait and don't go back.
In your publication cite :
NPS@: Network Protein Sequence Analysis
TIBS 2000 March Vol. 25, No 3 [291]:147-150
Combet C., Blanchet C., Geourjon C. and Deléage G.

CLUSTALW multiple alignment

Abstract Thompson, J.D., Higgins, D.G. and Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. (1994) Nucleic Acids Research, 22, 4673-4680 [HELP]
alignment with width :
residues.
Conservation level of % (works with "using conservation level of" option in list above).

with percentage of secondary structure.

DSC (King and Sternberg, 1996) (Do it alone) [HELP]
DPM (Deleage and Roux, 1987) [HELP]
GOR I (Garnier et al.,1978) Choose parameters [HELP]
GOR III (Gibrat et al.,1987) [HELP]
GOR IV (Garnier et al., 1996) [HELP]
HNN (Guermeur, 1997) [HELP]
SIMPA96 (Levin et al., 1996) [HELP]
PHD (Rost et al., 1994) (Do it alone) [HELP]
PREDATOR (Argos et al., 1996) Choose parameters [HELP]
SOPM (Geourjon and Deleage, 1994) (Do it alone) [Choose parameters] [HELP]
A prediction method with the Do it alone sentence must be the only newly selected one between two clicks on SHOW button. The other methods can be kept if they have been computed or can be added after. All methods can be displayed at the same time in the alignement.

View CLUSTALW in: [MPSA (Mac, UNIX) , About...] [AnTheProt (PC) , Download...] [HELP] 


                            10        20        30        40        50        60
                             |         |         |         |         |         |
UDELPATPK0073C10F   ------------------------GEPEEEEEEELVDPLTTIREHCEQTEKCVKARERLE
patpk0073c10f       VALPAGDPGSSRTAMGLRDTVVHAGEPEEEEEEELVDPLTTIREHCEQTEKCVKARERLE
pgn1cpk016l8        ---------------GLRDTVVHAGEPEEEEEEELVDPLTTIREHCEQTEKCVKARERLE
pgl1npk013n10       --------------MGLRDTVVHAGEPEEEEEEELVDPLTTIREHCEQTEKCVKARERLE
                                            ************************************
Prim.cons.          VALPAGDPGSSRTAMGLRDTVVHAGEPEEEEEEELVDPLTTIREHCEQTEKCVKARERLE

                            70        80        90       100       110       120
                             |         |         |         |         |         |
UDELPATPK0073C10F   LCDARVSSRSHTEEQCTEELFDFLHARDHCVAHKLFNKLK--------------------
patpk0073c10f       LCDARVSSRSHTEEQCTEELFDFLHARDHCVAHKLFNKLKMQELSICFYSPSEEPCRCTV
pgn1cpk016l8        LCDARVSSRSHTEEQCTEELFDFLHARDHCVAHKLFNKLKMQELSICFYSPSEEPCQCTV
pgl1npk013n10       LCDARVSSRSHTEEQCTEELFDFLHARDHCVAHKLFNKLKMQELSICFYSPSEEPCRCTV
                    ****************************************                    
Prim.cons.          LCDARVSSRSHTEEQCTEELFDFLHARDHCVAHKLFNKLKMQELSICFYSPSEEPCRCTV

                           130       140       150       160       170
                             |         |         |         |         |
UDELPATPK0073C10F   --------------------------------------------------------
patpk0073c10f       LLLPVYCQCEVQTKWLPGQLSTRMSCVCSSIEDCSYT-KTRGCS--CNSITLKFXV
pgn1cpk016l8        LLLPVYCQCEVQTKWLPGSDAPECRCVCS--HRCAATQKPCGCSVIFHIKHLKFLW
pgl1npk013n10       LLLPVYCQCEVQTKWLPGSDAPECRCVCS--HRCAATQKPRGCSVIFHIKHLKFLW
                                                                                
Prim.cons.          LLLPVYCQCEVQTKWLPGSDAPECRCVCSSIHRCAATQKPRGCSVIFHIKHLKFLW
Alignment data :
Alignment length : 176
Identity (*) : 76 is 43.18 %
Strongly similar (:) : 0 is 0.00 %
Weakly similar (.) : 0 is 0.00 %
Different : 100 is 56.82 %
Sequence 0001 : UDELPATPK0073C10F ( 76 residues).
Sequence 0002 : patpk0073c10f ( 173 residues).
Sequence 0003 : pgn1cpk016l8 ( 159 residues).
Sequence 0004 : pgl1npk013n10 ( 160 residues).
CLUSTALW options used :
endgaps=1
gapdist=8
gapext=0.2
gapopen=10.0
hgapresidues=GPSNDQERK
ktuple=1
matrix=gonnet
maxdiv=30
outorder=aligned
pairgap=3
score=percent
topdiags=5
type=PROTEIN
window=5
Result files (text) :
CLUSTALW
Garnier parameters

Auto calculated
Decision constants HelixSheetTurnCoil
Return


PREDATOR parameters

Secondary structure data
Return


SOPM parameters

Number of conformational states
Similarity threshold : Window width :
Return

SOPMA parameters

Number of conformational states
Similarity threshold : Window width :
Return

User : public@131.243.195.148. Last modification time : Mon Aug 4 02:18:29 2003. Current time : Mon Aug 4 02:18:29 2003 This service is supported by Ministere de la recherche (ACC-SV13), CNRS (IMABIO, COMI, GENOME) and Région Rhône-Alpes (Programme EMERGENCE) . Comments.