SVMSignal

SVMSignal help

INPUT

• SEQUENCE FORMAT
  Please input the protein sequence in FASTA format. Single-letter representation of 20 amino acids is accepted. Check your sequence before submitting to the program. The word following the character ">" is the title of the sequence.

  Both of the following examples could be accepted by SVMSignal:
  

  >P05979
  MSRQSISLRFPLLLLLLSPSPVFSADPGAPAPVNPCCYYPCQHQGICVRFGLDRYQCDCT
  RTGYSGPNCTIPEIWTWLRTTLRPSPSFIHFMLTHGRWLWDFVNATFIRDTLMRLVLTVR
  SNLIPSPPTYNIAHDYISWESFSNVSYYTRILPSVPRDCPTPMGTKGKKQLPDAEFLSRR
  FLLRRKFIPDPQGTNLMFAFFAQHFTHQFFKTSGKMGPGFTKALGHGVDLGHIYGDNLER
  QYQLRLFKDGKLKYQMLNGEVYPPSVEEAPVLMHYPRGIPPQSQMAVGQEVFGLLPGLML
  YATIWLREHNRVCDLLKAEHPTWGDEQLFQTARLILIGETIKIVIEEYVQQLSGYFLQLK
  FDPELLFGAQFQYRNRIAMEFNQLYHWHPLMPDSFRVGPQDYSYEQFLFNTSMLVDYGVE
  ALVDAFSRQPAGRIGGGRNIDHHILHVAVDVIKESRVLRLQPFNEYRKRFGMKPYTSFQE
  LTGEKEMAAELEELYGDIDALEFYPGLLLEKCHPNSIFGESMIEMGAPFSLKGLLGNPIC
  SPEYWKASTFGGEVGFNLVKTATLKKLVCLNTKTCPYVSFHVPDPRQEDRPGVERPPTEL
  

  >P05979
  MSRQSISLRF PLLLLLLSPS PVFSADPGAP APVNPCCYYP CQHQGICVRF GLDRYQCDCT
  RTGYSGPNCT IPEIWTWLRT TLRPSPSFIH FMLTHGRWLW DFVNATFIRD TLMRLVLTVR
  SNLIPSPPTY NIAHDYISWE SFSNVSYYTR ILPSVPRDCP TPMGTKGKKQ LPDAEFLSRR
  FLLRRKFIPD PQGTNLMFAF FAQHFTHQFF KTSGKMGPGF TKALGHGVDL GHIYGDNLER
  QYQLRLFKDG KLKYQMLNGE VYPPSVEEAP VLMHYPRGIP PQSQMAVGQE VFGLLPGLML
  YATIWLREHN RVCDLLKAEH PTWGDEQLFQ TARLILIGET IKIVIEEYVQ QLSGYFLQLK
  FDPELLFGAQ FQYRNRIAME FNQLYHWHPL MPDSFRVGPQ DYSYEQFLFN TSMLVDYGVE
  ALVDAFSRQP AGRIGGGRNI DHHILHVAVD VIKESRVLRL QPFNEYRKRF GMKPYTSFQE
  LTGEKEMAAE LEELYGDIDA LEFYPGLLLE KCHPNSIFGE SMIEMGAPFS LKGLLGNPIC
  SPEYWKASTF GGEVGFNLVK TATLKKLVCL NTKTCPYVSF HVPDPRQEDR PGVERPPTEL
  

• HOW TO SUBMIT
  Click on SUBMIT to send your request and a confirmation page will appear. The page will refresh itself every 30 seconds and display the result when prediction is finished. Please remember your job submission URL. The prediction results will be stored online for 30 days and discarded thereafter.

OUTPUT (example)

• PREDICTED RESULT
  Only top 100 residues and predicted states will display. The following is the description for the prediction result.

  Position	Protein sequence index
  Seq.	Protein sequence
  SVMSignal	The final predicted result from SVMSignal. Label 's' means the residue is a part of the signal peptide. Label 'C' means the last residue of the signal peptide. Label 'L' means the residue is not a part of the signal peptide.
  Cleavable	The first level predicted result from SVMSignal. Label 'C' means the potential cutting sites.

• PROFILE
  The calculated profile including free energy for convenience, amphiphilicity, charge index, polarity, and residue volume index will be drawn on the plane. The table also shows the physical-chemical properties of each residues.

• DOWNLOAD FILE
  The compressed file (SVMSignal.tar.gz) includes the AllPrediction.txt, AllCleavable.txt, and Profile.txt. If your query protein number is less than or equals to 500, the file will also include the profile images.