Example for submitting your alignment by email in MSF format

Bold face: keyword "# MSF"

Example for MSF format when using the WWW interface
Specification of compulsary features of MSF format.

The string "# MSF" is crucial, as the parser interprets anything after this line as an alignment in MSF format.
The '#' is a control for PredictProtein. The actual MSF-format begins after that line!
Names should contain up to 14 characters and no blanks.
Please use the same names for the same protein in all rows.
All sequences must have the same length.
To mark insertions, please use a point '.'.

Example

Joe Sequencer, Department of Advanced Protein Research,
National Univeristy, Timbuktu
joe@amino.churn.edu
# MSF   incredulase from paracoccus dementiae, translated from cDNA
***** don't type this line (is a comment): The hash ('#') is a control for PredictProtein.
***** don't type this line (is a comment): The actual MSF format starts in the next line.
MSF of: 9rnt.hssp from:    1 to:  104
 9rnt.msf  MSF:  104  Type: P 10-May-99  21:30:5  Check: 2138  ..
 

	please use the length identical for ALL sequences 
	
and let the length be the number of residues you have in the alignment
	

 Name: 9rnt0         Len:   104  Check: 5292  Weight:  1.00
 Name: rnt1_aspor    Len:   104  Check: 5442  Weight:  1.00
 Name: rnpc_pench    Len:   104  Check: 9918  Weight:  1.00
 Name: rnc2_aspcl    Len:   104  Check: 2103  Weight:  1.00
 Name: rnpb_penbr    Len:   104  Check: 1496  Weight:  1.00
 Name: rnms_aspsa    Len:   104  Check: 9117  Weight:  1.00
 Name: rnn1_neucr    Len:   104  Check: 1299  Weight:  1.00
 Name: rnf1_fusla    Len:   104  Check: 2764  Weight:  1.00
 Name: rnf1_fusmo    Len:   104  Check: 2593  Weight:  1.00
 Name: rnt1_triha    Len:   104  Check:  338  Weight:  1.00
 Name: rnf2_fusla    Len:   104  Check: 2426  Weight:  1.00
 Name: rnu1_ustsp    Len:   104  Check: 1288  Weight:  1.00
 Name: rnu2_ustsp    Len:   104  Check: 3893  Weight:  1.00
 Name: aga2_pedpe    Len:   104  Check: 4169  Weight:  1.00
 
//

The numbers are optional (i.e. NOT necessary) 
            1                                                   50  
9rnt0       ACDYTCGSNC YSSSDVSTAQ AAGYKLHEDG ETVGSNSYPH KYNNYEGFDF
rnt1_aspor  ACDYTCGSNC YSSSDVSTAQ AAGYQLHEDG ETVGSNSYPH KYNNYEGFDF
rnpc_pench  ACAATCGSVC YTSSAISAAQ EAGYDLYSAN DDVSN..YPH EYRNYEGFDF
rnc2_aspcl  .CDYTCGSHC YSASAVSDAQ SAGYQLESAG QSVGRSRYPH QYRNYEGFNF
rnpb_penbr  ACAATCGTVC YTSSAISSAQ AAGYNLYSTN DDVSN..YPH EYHNYEGFDF
rnms_aspsa  SCEYTCGSTC YWSSDVSAAK AKGYSLYESG DTIDD..YPH GYHDYEGFDF
rnn1_neucr  ACMYICGSVC YSSSAISAAL NKGYSYYEDG ATAGSSSYPH RYNNYEGFDF
rnf1_fusla  ....TCGSTP YSASQVRAAA NAACQYYQSD DTAGSTTYPH TYNNYEGFDF
rnf1_fusmo  ....TCGSTN YSASQVRAAA NAACQYYQND DSAGSTTYPH TYNNYEGFDF
rnt1_triha  ....TCGKVF YSASAVSAAS NAACNYVRAG STAGGSTYPH VYNNYEGFRF
rnf2_fusla  ....TCSSKP YSAQQVRAAA NAACQYYQSN DTAGSTTYPH TYHNYEGFDF
rnu1_ustsp  .....CGGTY YSSTQVNRA. ....INNAKS GQYSSTGYPH TYNNYEGFDF
rnu2_ustsp  .....CGGNV YSNDDINTAI QGALDDVANG DRPDN..YPH QYYAEASEDI
aga2_pedpe  .......... ...SYVIQIL AHRYPVhpYF EPMPSGSHAF ANDPTERFPY
 
            51                                                 100  
9rnt0       SVSSPYYEWP ILSSGDVYSG GSPGADRVVF NENNQLAGVI THTGASGNNF
rnt1_aspor  SVSSPYYEWP ILSSGDVYSG GSPGADRVVF NENNQLAGVI THTGASGNNF
rnpc_pench  PVSGTYYEFP ILRSGAVYSG NSPGADRVVF NGNDQLAGVI THTGASGNNF
rnc2_aspcl  PVSGNYYEWP ILSSGSTYNG GGPGADRVVF NDNDELAGLI THTGASGDGF
rnpb_penbr  PVSGTYYEFP ILKSGKVYTG SSPGADRVIF NDDDELAGVI THTGASGNNF
rnms_aspsa  PVSGTYYEYP IMSDYDVYTG GSPGADRVIF NGDDELAGVI THTGASGDDF
rnn1_neucr  PTAKPWYEFP ILSSGRVYTG GSPGADRVIF DSHGNLDMLI THNGASGNNF
rnf1_fusla  AVNGPYQEFP IRTGG.VYSG GSPGADRVII NTSCQYAGAI THTGASGNNF
rnf1_fusmo  PVDGPYQEFP IKSGG.VYTG GSPGADRVVI NTNCEYAGAI THTGASGNNF
rnt1_triha  klSKPFYEFP ILSSGKTYTG GSPGADRVVI NGQCSIAGII THTGASGNAF
rnf2_fusla  AVNGPYQEYP IRTSG.VYSG GSPGADRVII NTQCQFAGAI THTGASGNQF
rnu1_ustsp  SDygPYKEYP LKTSSSGYTG GSPGADRVVY DSNdtFCGAI THTGASGNNF
rnu2_ustsp  TlsGPWSEFP LVYNGPYYSS rsPGPDRVIY QTNteFCATV THTGAASYD.
aga2_pedpe  SVTSLPLEYS TIGS.....G DYRQPAYVIK DANNQLLPIL EYTGFSVND.
 
             104      
9rnt0       VECT
rnt1_aspor  VECT
rnpc_pench  VAC.
rnc2_aspcl  VAC.
rnpb_penbr  VACT
rnms_aspsa  VACS
rnn1_neucr  VAC.
rnf1_fusla  VGCS
rnf1_fusmo  VGCS
rnt1_triha  VAC.
rnf2_fusla  VGCS
rnu1_ustsp  VQCS
rnu2_ustsp  ....
aga2_pedpe  ....