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SSPAL Prediction of secondary structure Program Description Version 3.


Prediction of protein secondary structure by using local alignments. New, improved accuracy version with current PDB proteins was installed on October 3, 2001

Accuracy

Overall 3-state (a, b, c) prediction gives about 75% correctly predicted residues. THIS ACCURACY IS REACHED WITHOUT USING MULTIPLE ALIGNMENT INPUT when it is higher SEE ALSO "ssp" and "nssp" programs of this server.

Output results with probability of prediction:

Length=136
                    10        20        30        40        50
 PredSS       aaaaaaaaaaaa     aaaaaaaaaaa aaaa          aaaa 
 AA seq     LSADQISTVQASFDKVKGDPVGILYAVFKADPSIMAKFTQFAGKDLESIK
 ProbA      11999999999999111119999999999919999111111111199991
 ProbB      11000000000000111110000000000010000111111111100001
                    60        70        80        90       100
 PredSS       aaaaaaaaaaaaaaaaaaa     aaaaaaaaaaa      aaaaaaa
 AA seq     GTAPFETHANRIVGFFSKIIGELPNIEADVNTFVASHKPRGVTHDQLNNF
 ProbA      11999999999999999999911111999999999991111119999999
 ProbB      11000000000000000000011111000000000001111110000000
                   110       120       130
 PredSS     aaaaaaaaaaa      aaaaaaaaaaaaaaaaaa 
 AA seq     RAGFVSYMKAHTDFAGAEAAWGATLDTFFGMIFSKM
 ProbA      999999999991111119999999999999999991
 ProbB      000000000001111110000000000000000001

You can input multiple aligned sequences (now only in local version or email servers)

  • 1 line - sequence name
  • 2 line - number of aligned sequences and length of protein
  • 3 and subsequent lines - aligned sequences in format 60a1
  • (where 3-d line is empty or with numbers as well as other lines
  • which separate parts of aligned sequences)

The number of aligned sequences must be less than 250 !!!

 

for example:

     ACTINOXANTHIN                                                         
         5  107
             10        20        30        40        50        60 (numbers not    
     APAFSVSPASGASDGQSVSVSVAAAGETYYIAQaAPVGGQDAaNPATATSFTTDASGAAS  necessary) 
     APAFSVSPASGLSDGQSVSVSGAAAGETYYIAQCAPVGGQDACNPATATSFTTDASGAAS
     APTATVTPSSGLSDGTVVKVAGAgaGTAYDVGQCAWVdgVLACNPADFSSVTADANGSAS
     APGVTVTPATGLSNGQTVTVSATgpGTVYHVGQCAVvpGVIGCDATTSTDVTADAAGKIT
     ATPKSSSGGAGASTGSGTSSAAVTSgaASSAQQSGLQGATGAGGGSSSTPGTQPGSGAGG
             70        80        90       100      
     FSFTVRKSYAGQTPSGTPVGSVDbATDAbNLGAGNSGLNLGHVALTF
     FSFV-RKSYAGZTPSGTPVGSVDCATDACNLGAGNSGLNLGHVALTF
     TSLTVRRSFEGFLFDGTRWGTVDCTTAACQVGLSDAAGNGpgVAISF
     AQLKVHSSFQAVvaNGTPWGTVNCKVVSCSAGLGSDSGEGAAQAITF
     AIAARPVSAMGGtpPHTVPGSTNTTTTAMAGGVGGPgaNPNAAALM-
      
     (you can use small letters for Cys amino acids, if you want)

     Alignment MUST be without  deletions in the 1-st (query) sequence!!!

Reference:

Salamov A.A., Solovyev V.V.
Protein secondary sturcture prediction using local alignments.
J.Mol.Biol.1977, 268,1, 31-36.

Salamov A.A., Solovyev V.V.
Prediction of protein secondary sturcture by combining nearest-neighbor algorithms and multiply sequence alignments.
J.Mol.Biol.1995,247,1,11-15.


New version is implemented in collaboration with Drs. A. Bachinskiy and V. Ivanisenko

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