NPS@ : CLUSTALW ALIGNMENT

NPS@ is the IBCP contribution to PBIL in Lyon, France

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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: 4774) is running on NPS@ server (started on Mon Aug 4 02:44:23 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).

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


                      10        20        30        40        50        60
                       |         |         |         |         |         |
604160086F1   ----------AGATGGCGCTGCTCCGGCAGGCGTACAGCGCGCTCTTCCGCCGCACCTCC
604156339F1   --------------------GCTCCGGCAGGCGTACAGCGCGCTCTTCCGCCGCACCTCC
603405890F1   -----------------------CCGGCAGGCGTACAGCGCGCTCTTCCGCCGCACCTCC
603802382F1   GGCGCTTCCAAGATGGCGCTGCTCCGGCAGGCGTACAGCGCGCTCTTCCGCCGCACCTCC
603157981F1   -----------------TCTGCTCCGGCAGGCGT-CAGCGCGCTCTTCCGCCGCACCTCC
603742535F1   ----------AGATGGCGCTGCTCCGGCAGGCGTACAGCGCGCTCTTCCGCCGCACCTCC
603577656F1   -GCGCTTCCAAGATGGCGCTGCTCCGGCAGGCGTACAGCGCGCTCTTCCGCCGCACCTCC
603208289F1   ---------------------ATCCGGCAGGCGTACAGCGCGCTCTTCCGCCGCACCTCC
604147186F1   --------------------CCTCCGGCAGGCGTACAGCGCGCTCTTCCGCCGCACCTCC
603210295F1   ------------------------------------------------------------
                                                                          
Prim.cons.    GGCGCTTCCAAGATGGCGCTGCTCCGGCAGGCGTACAGCGCGCTCTTCCGCCGCACCTCC

                      70        80        90       100       110       120
                       |         |         |         |         |         |
604160086F1   ACTTTCGCCCTCACCGTCGTGCTGGGCGCCGTGCTGTTCGAGCGCGCCTTCGATCAGGGC
604156339F1   ACTTTCGCCCTCACCGTCGTGCTGGGCGCCGTGCTGTTCGAGCGCGCCTTCGATCAGGGC
603405890F1   ACTTTCGCCCTCACCGTCGTGCTGGGCGCCGTGCTGTTCGAGCGCGCCTTCGATCAGGGC
603802382F1   ACTTTCGCCCTCACCGTCGTGCTGGGCGCCGTGCTGTTCGAGCGCGCCTTCGATCAGGGC
603157981F1   ACTTTCGCCCTCACCGTCGTGCTGGGCGCCGTGCTGTTCGAGCGCGCCTTCGATCAGGGC
603742535F1   ACTTTCGCCCTCACCGTCGTGCTGGGCGCCGTGCTGTTCGAGCGCGCCTTCGATCAGGGC
603577656F1   ACTTTCGCCCTCACCGTCGTGCTGGGCGCCGTGCTGTTCGAGCGCGCCTTCGATCAGGGC
603208289F1   ACTTTCGCCCTCACCGTCGTGCTGGGCGCCGTGCTGTTCGAGCGCGCCTTCGATCAGGCC
604147186F1   ACTTTCGCCCTCACCGTCGTGCTGGGCGCCGTGCTGTTCGAGCGCGCCTTCGATCAGGGC
603210295F1   ------------------------------------------------------------
                                                                          
Prim.cons.    ACTTTCGCCCTCACCGTCGTGCTGGGCGCCGTGCTGTTCGAGCGCGCCTTCGATCAGGGC

                     130       140       150       160       170       180
                       |         |         |         |         |         |
604160086F1   GCCGACGCCATCTTCGAGCACCTCAACGAGGGGAAACTGTGGAAACACATCAAGCACAAA
604156339F1   GCCGACGCCATCTTCGAGCACCTCAACGAGGGGAAACTGTGGAAACACATCAAGCACAAA
603405890F1   GCCGACGCCATCTTCGAGCACCTCAACGAGGGGAAACTGTGGAAACACATCAAGCACAAA
603802382F1   GCCGACGCCATCTTCGAGCACCTCAACGAGGGGAAACTGTGGAAACACATCAAGCACAAA
603157981F1   GCCGACGCCATCTTCGAGCACCTCAACGAGGGGAAACTGTGGAAACACATCAAGCACAAA
603742535F1   GCCGACGCCATCTTCGAGCACCTCAACGAGGGGAAACCGTGGAAACACATCAAGCACAAA
603577656F1   GCCGACGCCATCTTCGAGCACCTCAACGAGGGGAAACTGTGGAAACACATCAAGCACAAA
603208289F1   GCCGACGCCATCTTCGAGCACCTCAACGAGGGGAAACTGTGGAAACACATCAAGCACAAA
604147186F1   GCCGACGCCATCTTCGAGCACCTCAACGAGGGGAAACTGTGGAAACACATCAAGCACAAA
603210295F1   -------------------------------GGAAACTGTGGAAACACATCAAGCACAAA
                                             ****** **********************
Prim.cons.    GCCGACGCCATCTTCGAGCACCTCAACGAGGGGAAACTGTGGAAACACATCAAGCACAAA

                     190       200       210       220       230       240
                       |         |         |         |         |         |
604160086F1   TACGAGGCAAGTGAAGAGTGAAATGCTCAGCAGCAAGATCCAGTCTGGGGTGGCAAAAGA
604156339F1   TACGAGGCAAGTGAAGAGTGAAATGCTCAGCAGCAAGATCCAGTCTGGGGTGGCAAAAGA
603405890F1   TACGAGGCAAGTGAAGAGTGAAATGCTCAGCAGCAAGATCCAGTCTGGGGTGGCAAAAGA
603802382F1   TACGAGGCAAGTGAAGAGTGAAATGCTCAGCAGCAAGATCCAGTCTGGGGTGGCAAAAGA
603157981F1   TACGAGGCAAGTGAAGAGTGAAATGCTCAGCAGCAAGATCCAGTCTGGGGTGGCAAAAGA
603742535F1   TACGAGGCAAGTGAAGAGTGAAATGCTCAGCAGCAAGATCCAGTCTGGGGTGGCAAAAGA
603577656F1   TACGAGGCAAGTGAAGAGTGAAATGCTCAGCAGCAAGATCCAGTCTGGGGTGGCAAAAGA
603208289F1   TACGAGGCAAGTGAAGAGTGAAATGCTCAGCAGCAAGATCCAGTCTGGGGTGGCAAAAGA
604147186F1   TACGAGGCAAGTGAAGAGTGAAATGCTCAGCAGCAAGATCCAGTCTGGGGTGGCAAAAGA
603210295F1   TACGAGGCAAGTGAAGAGTGAAATGCTCAGCAGCAAGATCCAGTCTGGGGTGGCAAAAGA
              ************************************************************
Prim.cons.    TACGAGGCAAGTGAAGAGTGAAATGCTCAGCAGCAAGATCCAGTCTGGGGTGGCAAAAGA

                     250       260       270       280       290       300
                       |         |         |         |         |         |
604160086F1   CACTGCAGAGAAGGATTCAGTCTCCTGAAACGGGTTGTACTGAAA-TGGAATTGGGTCCC
604156339F1   TACTGCAGAGAAGGATTCAGTCTCCTGAAACGGGTTGTACTGAAA-TGGAATTGGGTCCC
603405890F1   CACTGCAGAGAAGGATTCAGTCTCCTGAAACGGGTTGTACTGAAA-TGGAATTGGGTCCC
603802382F1   CACTGCAGAGAAGGATTCAGTCTCCTGAAACGGGTTGTACTGAAA-TGGAATTGGGTCCC
603157981F1   CACTGCAGAGAAGGATTCAGTCTCCTGAAACGGGTTGTACTGAAA-TGGAATTGGGTCCC
603742535F1   CACTGCAGAGAAGGATTCAGTCTCCTGAAACGGGTTGTACTGAAA-TGGAATTGGGTCCC
603577656F1   CACTGCAGAGAAGGATTCAGTCTCCTGAAACGGGTTGTACTGAAAGTGGAATGGGGTCCC
603208289F1   CACTGCAGAGAAGGATTCAGTCTCCTGAAACGGGTTGTACTGAAA-TGGAATTGGGTCCC
604147186F1   CACTGCAGAGAAGGATTCAGTCTCCTGAAACGGGTTGTACTGAAA-TGGAATTGGGTCCC
603210295F1   CACTGCAGAGAAGGATTCAGTCTCCTGAAACGGGTTGTACTGAAA-TGGAATTGGGTCCC
               ******************************************** ****** *******
Prim.cons.    CACTGCAGAGAAGGATTCAGTCTCCTGAAACGGGTTGTACTGAAAGTGGAATTGGGTCCC

                     310       320       330       340       350       360
                       |         |         |         |         |         |
604160086F1   TGAC-TGACTCCGAGCCAGATTATATCAGCCACCTACTGATATGATGTCAACCAAGATGG
604156339F1   TGAC-TGACTCCGAGCCAGATTATATCAGCCACCTACTGATATGATGTCAACCAAGATGG
603405890F1   TGAC-TGACTCCGAGCCAGATTATATCAGCCACCTACTGATATGATGTCAACCAAGATGG
603802382F1   TGAC-TGACTCCGAGCCAGATTATATCAGCCACCTACTGATATGATGTCAACCAAGATGG
603157981F1   TGAC-TGACTCCGAGCCAGATTATATCAGCCACCTACTGATATGATGTCAACCAAGATGG
603742535F1   TGAC-TGACTCCGAGCCAGATTATATCAGCCACCTACTGATATGATGTCAACCAAGATGG
603577656F1   TGACGTGACTCCGAGCCAGATTATATCAGCCACCTACTGATATGATGTCAACCAAGATGG
603208289F1   TGAC-TGACTCCGAGCCAGATTATATCAGCCACCTACTGATATGATGTCAACCAAGATGG
604147186F1   TGAC-TGACTCCGAGCCAGATTATATCAGCCACCTACTGATATGATGTCAACCAAGATGG
603210295F1   TGAC-TGACTCCGAGCCAGATTATATCAGCCACCTACTGATATGATGTCAACCAAGATGG
              **** *******************************************************
Prim.cons.    TGACGTGACTCCGAGCCAGATTATATCAGCCACCTACTGATATGATGTCAACCAAGATGG

                     370       380       390       400       410       420
                       |         |         |         |         |         |
604160086F1   ACTCAACGAGTTCTGCTGCTGTACTGAAACTTACTGTGTTCCAATAAAAAAAAAACAT-T
604156339F1   ACTCAACGAGTTCTGCTGCTGTACTGAAACTTACTGTGTTCCAATAAAAAAAAAACAC-T
603405890F1   ACTCAACGAGTTCTGCTGCTGTACTGAAACTTACTGTGTTCCAATAAAAAAAAC-CAT-T
603802382F1   ACTCAACGAGTTCTGCTGCTGTACTGAAACTTACTGTGTTCCAATAAAAAAAAC-CAT-C
603157981F1   ACTCAACGAGTTCTGCTGCTGTACTGAAACTTACTGTGTTCCAATAAAAAAACC-CAT-T
603742535F1   ACTCAACGAGTTCTGCTGCTGTACTGAAACTTACTGTGTTCCAATAAAAAAACC-CATTC
603577656F1   ACTCAACGAGTTCTGCTGCTGTACTGAAACTTACTGTGTTCCAATAAAAAAACC-CA--C
603208289F1   ACTCAACGAGTTCTGCTGCTGTACTGAAACTTACTGTGTTCCAATAAAAAAAAC-CAT-C
604147186F1   ACTCAACGAGTTCTGCTGCTGTACTGAAACTTACTGTGTTCCAATAAAAAAACC-CAT-T
603210295F1   ACTCAACGAGTTCTGCTGCTGTACTGAAACTTACTGTGTTCCAATAAAAAAACC-CATTC
              ****************************************************   **   
Prim.cons.    ACTCAACGAGTTCTGCTGCTGTACTGAAACTTACTGTGTTCCAATAAAAAAA2CACATT2

                     430       440       450       460
                       |         |         |         |
604160086F1   CTTCAAAAA-----------------------------------
604156339F1   CT-CAAAAA-----------------------------------
603405890F1   CTCCAAAAA-----------------------------------
603802382F1   CTCGAAAAA-----------------------------------
603157981F1   CTGGAAAAA-----------------------------------
603742535F1   CCGTAAAAA-----------------------------------
603577656F1   CCTTAAAAA-----------------------------------
603208289F1   CCTGAAAAA-----------------------------------
604147186F1   CCTGAAAAA-----------------------------------
603210295F1   CTGAAAAAAAAAAAAACAAAAAACTCTAGTCGCGATCTAGAACA
              *   *****                                                   
Prim.cons.    CTTGAAAAAAAAAAAACAAAAAACTCTAGTCGCGATCTAGAACA

Alignment data :
Alignment length : 464
Identity (*) : 264 is 56.90 %
Strongly similar (:) : 0 is 0.00 %
Weakly similar (.) : 0 is 0.00 %
Different : 200 is 43.10 %
Sequence 0001 : 604160086F1 ( 416 residues).
Sequence 0002 : 604156339F1 ( 405 residues).
Sequence 0003 : 603405890F1 ( 402 residues).
Sequence 0004 : 603802382F1 ( 425 residues).
Sequence 0005 : 603157981F1 ( 407 residues).
Sequence 0006 : 603742535F1 ( 416 residues).
Sequence 0007 : 603577656F1 ( 425 residues).
Sequence 0008 : 603208289F1 ( 404 residues).
Sequence 0009 : 604147186F1 ( 405 residues).
Sequence 0010 : 603210295F1 ( 310 residues).

CLUSTALW options used :
dnamatrix=iub
endgaps=1
gapdist=8
gapext=0.05
gapopen=10.0
ktuple=1
maxdiv=40
outorder=aligned
pairgap=3
score=percent
topdiags=5
type=DNA
window=5

Result files (text) :
CLUSTALW

User : public@131.243.195.148. Last modification time : Mon Aug 4 02:44:26 2003. Current time : Mon Aug 4 02:44:26 2003 This service is supported by Ministere de la recherche (ACC-SV13), CNRS (IMABIO, COMI, GENOME) and Région Rhône-Alpes (Programme EMERGENCE) . Comments.