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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: 6470) is running on NPS@ server (started on Mon Aug 4 03:05:02 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
                              |         |         |         |         |         |
603157981F1          ------SAPAGVSALFRRTSTFALTVVLGAVLFERAFDQGADAIFEHLNEGKLWKHIKHK
603210295F1          ---------------------------------------------------KLWKHIKHK
604147186F1          -------LRQAYSALFRRTSTFALTVVLGAVLFERAFDQGADAIFEHLNEGKLWKHIKHK
603742535F1          ----MALLRQAYSALFRRTSTFALTVVLGAVLFERAFDQGADAIFEHLNEGKPWKHIKHK
603405890F1          --------RQAYSALFRRTSTFALTVVLGAVLFERAFDQGADAIFEHLNEGKLWKHIKHK
603802382F1          GASKMALLRQAYSALFRRTSTFALTVVLGAVLFERAFDQGADAIFEHLNEGKLWKHIKHK
603208289F1          -------IRQAYSALFRRTSTFALTVVLGAVLFERAFDQAADAIFEHLNEGKLWKHIKHK
604156339F1          -------LRQAYSALFRRTSTFALTVVLGAVLFERAFDQGADAIFEHLNEGKLWKHIKHK
604160086F1          ----MALLRQAYSALFRRTSTFALTVVLGAVLFERAFDQGADAIFEHLNEGKLWKHIKHK
UDELPNF_BPK00002B9   ------LLRQAYSALFRRTSTFALTVVLGAVLFERAFDQGADAIFEHLNEGKLWKHIKHK
603577656F1          -ASKMALLRQAYSALFRRTSTFALTVVLGAVLFERAFDQGADAIFEHLNEGKLWKHIKHK
                                                                        * *******
Prim.cons.           GASKMALLRQAYSALFRRTSTFALTVVLGAVLFERAFDQGADAIFEHLNEGKLWKHIKHK

                             70        80        90       100       110       120
                              |         |         |         |         |         |
603157981F1          YEASEENAQQQDPVWGGKRHCREGFSLLKRVVLKWNWVPDLRARLYQPPTDMMSTKMDST
603210295F1          YEASEENAQQQDPVWGGKRHCREGFSLLKRVVLKWNWVPDLRARLYQPPTDMMSTKMDST
604147186F1          YEASEENAQQQDPVWGGKRHCREGFSLLKRVVLKWNWVPDLRARLYQPPTDMMSTKMDST
603742535F1          YEASEENAQQQDPVWGGKRHCREGFSLLKRVVLKWNWVPDLRARLYQPPTDMMSTKMDST
603405890F1          YEASEENAQQQDPVWGGKRHCREGFSLLKRVVLKWNWVPDLRARLYQPPTDMMSTKMDST
603802382F1          YEASEENAQQQDPVWGGKRHCREGFSLLKRVVLKWNWVPDLRARLYQPPTDMMSTKMDST
603208289F1          YEASEENAQQQDPVWGGKRHCREGFSLLKRVVLKWNWVPDLRARLYQPPTDMMSTKMDST
604156339F1          YEASEENAQQQDPVWGGKRYCREGFSLLKRVVLKWNWVPDLRARLYQPPTDMMSTKMDST
604160086F1          YEASEENAQQQDPVWGGKRHCREGFSLLKRVVLKWNWVPDLRARLYQPPTDMMSTKMDST
UDELPNF_BPK00002B9   YEASE-------------------------------------------------------
603577656F1          YEASEENAQQQDPVWGGKRHCREGFSLLKRVVLKVEWGPRDSEPDYI--SHLLICQPRWT
                     *****                                                       
Prim.cons.           YEASEENAQQQDPVWGGKRHCREGFSLLKRVVLKWNWVPDLRARLYQPPTDMMSTKMDST

                            130       140       150
                              |         |         |
603157981F1          SSAAVLK-LTVFQKNPFWK------------
603210295F1          SSAAVLK-LTVFQKNPFLKKKKTKNSSRDLE
604147186F1          SSAAVLK-LTVFQKNPFLK------------
603742535F1          SSAAVLK-LTVFQKNPFPK------------
603405890F1          SSAAVLK-LTVFQKKPFSK------------
603802382F1          SSAAVLK-LTVFQKKPSSK------------
603208289F1          SSAAVLK-LTVFQKKPSLK------------
604156339F1          SSAAVLK-LTVFQKKNTLK------------
604160086F1          SSAAVLK-LTVFQKKNILQK-----------
UDELPNF_BPK00002B9   -------------------------------
603577656F1          QRVLLLYNLLCSNKKTHPK------------
                                                                                 
Prim.cons.           SSAAVLKNLTVFQKKPFLKKKKTKNSSRDLE
Alignment data :
Alignment length : 151
Identity (*) : 13 is 8.61 %
Strongly similar (:) : 0 is 0.00 %
Weakly similar (.) : 0 is 0.00 %
Different : 138 is 91.39 %
Sequence 0001 : 603157981F1 ( 132 residues).
Sequence 0002 : 603210295F1 ( 99 residues).
Sequence 0003 : 604147186F1 ( 131 residues).
Sequence 0004 : 603742535F1 ( 134 residues).
Sequence 0005 : 603405890F1 ( 130 residues).
Sequence 0006 : 603802382F1 ( 138 residues).
Sequence 0007 : 603208289F1 ( 131 residues).
Sequence 0008 : 604156339F1 ( 131 residues).
Sequence 0009 : 604160086F1 ( 135 residues).
Sequence 0010 : UDELPNF_BPK00002B9 ( 59 residues).
Sequence 0011 : 603577656F1 ( 136 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 03:05:05 2003. Current time : Mon Aug 4 03:05:05 2003 This service is supported by Ministere de la recherche (ACC-SV13), CNRS (IMABIO, COMI, GENOME) and Région Rhône-Alpes (Programme EMERGENCE) . Comments.