When you see in NPS@ the sentence "Paste a profile HMM in HMMER format below", you must paste a profile HMM as indicated below.

PROFILE HMM IN HMMER FORMAT :

HMMER2.0  [2.2g]
NAME  20416
LENG  17
ALPH  Amino
RF    no
CS    no
MAP   yes
COM   /pbil/bin/hmmer/hmmbuild --wgsc --pbswitch 1000 /pbil/servers/npsa/www/tmp/20416.hmm /pbil/servers/npsa/www/tmp/20416.clustal
COM   /pbil/bin/hmmer/hmmcalibrate --mean 350 --num 5000 --sd 350 --cpu 2 /pbil/servers/npsa/www/tmp/20416.hmm
NSEQ  6
DATE  Mon Feb  3 16:50:56 2003
CKSUM 4635
XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4 
NULT      -4  -8455
NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -1085   -142    -21   -313     45    531    201    384  -1998   -644 
EVD   -10.794779   0.395599
HMM        A      C      D      E      F      G      H      I      K      L      M      N      P      Q      R      S      T      V      W      Y    
         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
         -507      *  -1754
     1   -476  -1145   1421    -20  -1092  -1337   -343   -583   -229   -738   3360   -253  -1588    -91   -638   -558   -480   -487  -1523   -975     4
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -27  -6312  -7354   -894  -1115   -701  -1378   -507      * 
     2   -349  -1556    898    289  -1795  -1311    -21  -1478   1350  -1542   2455     -1  -1431    392   -117    554   -295  -1138  -1811  -1194     5
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -19  -6808  -7850   -894  -1115   -701  -1378      *      * 
     3   -601  -1821   -314     91  -2254  -1440   -152  -1929   2135  -1910  -1069   1795  -1604    268    117   -511    858  -1541  -2075  -1504     6
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -19  -6808  -7850   -894  -1115   -701  -1378      *      * 
     4  -1093   -835  -3338  -2782   -882  -2841  -1854   2471  -2480   -241   2553  -2430  -2820  -2169  -2400  -1970    970   1427  -1694  -1352     7
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -7108  -8150   -894  -1115   -701  -1378      *      * 
     5   -986  -1763  -1222   -861  -2585  -1777   -824  -2121   1694  -2250  -1528   -933  -2100   -474   -199  -1039   2979  -1759  -2454  -2055     8
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -7108  -8150   -894  -1115   -701  -1378      *      * 
     6  -2071  -1630  -4432  -3973   -914  -4128  -3239   3168  -3705   1440    241  -3777  -3785  -3188  -3557  -3412  -2019    550  -2451  -2274     9
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -7108  -8150   -894  -1115   -701  -1378      *      * 
     7  -2043  -2655   1856   -921   -319  -2320   -870  -2657  -1754  -2485  -2126  -1127  -2699  -1338  -2200  -1894  -2082  -2492   -954   4076    10
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -7108  -8150   -894  -1115   -701  -1378      *      * 
     8  -1781  -3655   3361   1791  -3844  -1644  -1035  -3795  -1330  -3668  -3038   -247  -2195   -716  -2210  -1430  -1861  -3271  -3827  -2821    11
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -7108  -8150   -894  -1115   -701  -1378      *      * 
     9  -1745  -1304  -4274  -3840  -1405  -3948  -3322   2118  -3663    974   -225  -3586  -3729  -3363  -3638  -3208  -1714   2740  -2806  -2485    12
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -7108  -8150   -894  -1115   -701  -1378      *      * 
    10   3438  -1472  -2846  -3040  -3287  -1726  -2735  -2840  -3028  -3257  -2662  -2236  -2447  -2798  -2944  -1216  -1387  -2183  -3405  -3320    13
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -7108  -8150   -894  -1115   -701  -1378      *      * 
    11  -1470  -2528  -1412   1151  -3129  -2169   -408  -2639   1671  -2415  -1653   -820  -2204     21   2944  -1342  -1287  -2320  -2377  -2060    14
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -7108  -8150   -894  -1115   -701  -1378      *      * 
    12    715  -1317   -668   1742  -1404  -1664   -554   -841   -353   1308   -468   -565  -1846   -276   -738   -759   -637   -704  -1757  -1264    15
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -7108  -8150   -894  -1115   -701  -1378      *      * 
    13   3009   -931  -2474  -2519  -3072  -1199  -2265  -2764  -2485  -3067  -2216  -1652  -1946  -2192  -2502   1357   -737  -1841  -3317  -3073    16
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -7108  -8150   -894  -1115   -701  -1378      *      * 
    14   -568  -1344   -875  -1008  -3106   2886  -1527  -2907  -1548  -3040  -2198   1153  -1950  -1267  -1918    761   -898  -2074  -3233  -2743    17
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -7108  -8150   -894  -1115   -701  -1378      *      * 
    15  -1771  -1603  -3750  -3689  -2037  -3050  -3231    403  -3479  -1154  -1076  -3246  -3399  -3383  -3437  -2628  -1917   3536  -3074  -2677    18
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -7108  -8150   -894  -1115   -701  -1378      *      * 
    16   -897  -1462  -2333  -2543  -3185  -1640  -2474  -3294  -2686  -3497  -2780  -1973  -2360  -2483  -2703   3465  -1316  -2413  -3310  -3025    19
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -720    275    394     45     96    359    117   -369   -294   -249 
     -    -16  -7108  -8150   -894  -1115   -701  -1378      *      * 
    17    779   -624  -1797  -1208   -597  -1908   -719   1149   -867   -350   2905  -1152  -1976   -768   1209   -950   -480     70  -1082   -707    20
     -      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      *      * 
     -      *      *      *      *      *      *      *      *      0 
//


To obtain a profile HMM in HMMER format, you have to use HMMBUILD.

For further details about this format, see HMMER User's Guide.


User : public@35.170.81.210. Last modification time : Fri Feb 11 10:13:06 2011. Current time : Fri Dec 6 19:27:28 2019