Example for requesting to return the 1D structure prediction in MSF format

Bold face: keyword "return phd msf"

Input (request of you)

Joe Sequencer, Department of Advanced Protein Research,
National Univeristy, Timbuktu
joe@amino.churn.edu
return phd msf   
# sh3 
KELVLALYDYQEKSPREVTMKKGDILTL
LNSTNKDWWKVEVNDRQGFVPAAYVKKLD

Output (result returned)

• Block with sequence alignment.
• Block with information about prediction method.
• Block with prediction in default format.
• Block with alignment, and prediction in MSF format (shown here):

Explanations:

• 1st block Alignment
  • sequence identifier
  • residues (in chunks of 60 per line)
• 2nd block Predictions
  • AApred : sequence for which structure is predicted
  • PHDsec : secondary structure in three states: helix H, strand E, rest L
  • RELsec : reliability of secondary structure prediction scaled between 0 (low) and 9 (high)
  • SUBsec : subset of the prediction, for all residues with a reliability index RELsec ≥ 4, i.e., a subset for which the expected average accuracy is ≥ 88% (tables)
  • P_3acc : residue solvent accessibility in three states: buried b (< 9% relative accessibility), intermediate blank, and exposed e (> 25% relative accessibility)
  • RELacc : reliability of accessibility prediction scaled between 0 (low) and 9 (high)
  • SUBacc : subset of the prediction, for all residues with a reliability index RELacc ≥ 3, i.e., a subset for which the expected average accuracy is ≥ 90% (tables)
  • PHDacc : relative residue solvent accessibility ≤ n**2, i.e., the square of the number given per residue provides a lower limit for the relative accessibility

PHD prediction and alignment in MSF format

                 ....,....1....,....2....,....3....,....4....,....5....,....6
 t3_27793        KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGFVPAAYVKKLD
 spcn_chick      KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGFVPAAYVKKLD
 spca_drome      KECVVALYDYTEKSPREVSMKKGDVLTLLNSNNKDWWKVEVNDRQGFVPAAYIKKID
 foda_mouse      ..........................ALLNSTNKDWWKVEVNDRQGFVPAAYVKKLD
 spca_human      EQRVMALYDFQARSPREVTMKKGDVLTLLSSINKDWWKVEAADHQGIVPAVYVRRL.
 blk_human       KHFVVALYDYTAMNDRDLQMLKGEKLQVLKGT.GDWWLArvTGREGYVPSNFVARVE
 mysd_dicdi      KPSAKALYDFDAESSMELSFKEGDILTVLDQSSGDWWDAELKGRRGKVPSNYLQLI.
 ps20_yeast      .EFARALYDFVPENpmEVALKKGDLMAILSKKdsDWWKVRtnGNIGYIPYNYIEII.
 mysc_acaca      PEQARALYDFAAENPDELTFNEGAVVTVINKSNPDWWEGELNGQRGVFPASYVELI.
 mysb_acaca      KPQVKALYDYDAQTGDELTFKEGDTIIVHQKDPAGWWEGELNGKRGWVPANYVQDI.
 cc15_schpo      .GYVIALYDYQAQIPEEISFQKGDTLMVLRTQEDGWWDGEinSKRGLFPSNFVQTV.
 blk_mouse       ERFVVALFDYAAVNDRDLQVLKGEKLQVLRST.GDWWLArvTGREGYVPSNFVAPVE
 itk_mouse       ETLVIALYDYQTNDPQELALRCDEEYYLLDSSEIHWWRVQdnGHEGYAPSSYL....
 yha2_yeast      ...VRALYDLTTNEPDELSFRKGDVITVLEQVYRDWWKGALRGNMGIFPLNYVTPI.
 itk_human       ETVVIALYDYQTNDPQELALRRNEEYCLLDSSEIHWWRVQdnGHEGYVPSSYL....
 crkl_human      .EYVRTLYDFPGNDAEDLPFKKGEILVIIEKPEEQWWSARNKdrVGMIPVPYVEKL.
 vav_human       .....ARYDFCARDRSELSLKEGDIIKILNKKgqGWWRGEIYGRVGWFPANYVEE..
 srcn_mouse      .TTFVALYDYESRTETDLSFKKGERLQIVNNTRkdWWLAHstGQTGYIPSNYVAPSD
 lyn_human       GDIVVALYPYDGIHPDDLSFKKGEKMKVLEEH.GEWWKAklTKKEGFIPSNYVAKLN
 fyn_xiphe       .TLFVALYDYEARTEDDLSFRKGERFQILNSTEGDWWDARstGGSGYIPSNYVAPVD
 fgr_human       .TLFIALYDYEARTEDDLTFTKGEKFHILNNTEGDWWEARssGKTGCIPSNYVAPVD
 lyn_rat         GDIVVALYPYDGIHPDDLSFKKGEKMKVLEEH.GEWWKAKssKREGFIPSNYVAKVN
 lyn_mouse       GDIVVALYPYDGIHPDDLSFKKGEKMKVLEEH.GEWWKAKssKREGFIPSNYVAKVN
 fgr_mouse       .TIFVALYDYEARTGDDLTFTKGEKFHILNNTEYDWWEARssGHRGYVPSNYVAPVD

  PREDICTIONS:
 AApred          .ELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGFVPAAYVKKLD
 PHDsec          . EEEEEEE        EEE    EEEEE       EEE      EEE    EEE
 RELsec          .38999982488784212444897899847898332566256983211221221149
 SUBsec          ..EEEEEE..LLLL.......LLLEEEE.LLLL...EEE.LLLL............L
 P_3acc          .ebbbbbbebeeeeeeebebeebeebebbeeeeeebbebeeeeeebbbbbebbeebe
 RELacc          .51739931133514542125503152644544531343225444303313251407
 SUBacc          .e.b.bb.....e.eee...ee...b.bbeeeee...e...eeee.......b.e.e
 PHDacc          .70000006077767770607707606007777770070677777000007006709