CSC334 Psipred E-coli AAF33488

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This is a log of the interaction with Psipred for the following sequence:

• Protein Reference Number: AAF33488 (E Coli)

• Sequence in FASTA (no first line)

MESTVDTELLKTFLEVSRTRHFGRAAEALYLTQSAVSFRIRQLENQLGVNLFTRHRNNIRLTTAGEKLLP
YAETLMNTWQAARKEVAHTSRHNEFSIGASASLWECMLNAWLGRLYQLQEPQSGLQFEARIAQRQSLVKQ
LHERQLDLLITTEAPKMDEFSSQLLGHFTLALYCSSPARKKSELNYLRLEWGPDFQQHETGLIAADEVPV
LTTSSAELARQQLSALNGCSWLPVNWANEKGGLHTVADSATLSRPLYAIWLQNSDKYSLICDLLKTDVLD
EQ

• Response on Web browser from Psipred

Your PSIPRED job has been submitted.
Results will be sent to: thiebaut@cs.smith.edu

Number of jobs currently in queue: 0

Thank you for using the PSIPRED server.

• email received (Be careful to check your junk and quarantine areas. The message sent by the server is from user Apache which some mail system might automatically assume is junk mail.)

PSIPRED PREDICTION RESULTS

Key

Conf: Confidence (0=low, 9=high)
Pred: Predicted secondary structure (H=helix, E=strand, C=coil)
  AA: Target sequence

    
# PSIPRED HFORMAT (PSIPRED V2.6 by David Jones)

Conf: 999888999999999998399899999967888489999999999829843897699436
Pred: CCCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCEEEEECCCCEE
  AA: MESTVDTELLKTFLEVSRTRHFGRAAEALYLTQSAVSFRIRQLENQLGVNLFTRHRNNIR
              10        20        30        40        50        60


Conf: 988799999999999999999999987316873499996345677768999999999785
Pred: ECHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEHHHHHHHHHHHHHHHHHHHH
  AA: LTTAGEKLLPYAETLMNTWQAARKEVAHTSRHNEFSIGASASLWECMLNAWLGRLYQLQE
              70        80        90       100       110       120


Conf: 589818999988999999999859966899837989998179998605579984885212
Pred: HCCCEEEEEEECCHHHHHHHHHCCCCCEEEEECCCCCCCEEEEEEEECCEEEEECCCCCC
  AA: PQSGLQFEARIAQRQSLVKQLHERQLDLLITTEAPKMDEFSSQLLGHFTLALYCSSPARK
             130       140       150       160       170       180


Conf: 688995770578769999999534269977997829999999992898798469998546
Pred: CCCCCEEEECCCCHHHHHHHHHHHHCCCCEEEECHHHHHHHHHHHCCCEEEEEHHHHHHC
  AA: KSELNYLRLEWGPDFQQHETGLIAADEVPVLTTSSAELARQQLSALNGCSWLPVNWANEK
             190       200       210       220       230       240


Conf: 988943789986148999995899707999999998764059
Pred: CCEEECCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHCC
  AA: GGLHTVADSATLSRPLYAIWLQNSDKYSLICDLLKTDVLDEQ
             250       260       270       280


Calculate PostScript, PDF and JPEG graphical output for this result using: 
http://bioinf3.cs.ucl.ac.uk/cgi-bin/psipred/gra/nph-view2.cgi?id=ab6766dd548c0639.psi

• Clicking on http://bioinf3.cs.ucl.ac.uk/cgi-bin/psipred/gra/nph-view2.cgi?id=ab6766dd548c0639.psi brings up the following Web page:

PSIPREDView

Graphical output for PSIPRED predictions


Liam J. McGuffin, Kevin Bryson and David T. Jones

Bioinformatics Group, Department of Computer Science,
University College London, Gower Street, London WC1E 6BT, UK
Click on the links below to view your results.
Format 	Location
PostScript File 	http://bioinf3.cs.ucl.ac.uk/psiout/ab6766dd548c0639.psi.ps
PDF File	http://bioinf3.cs.ucl.ac.uk/psiout/ab6766dd548c0639.psi.pdf
JPEG Page 1 	http://bioinf3.cs.ucl.ac.uk/psiout/ab6766dd548c0639.psi_1.jpg
JPEG Page 2 	http://bioinf3.cs.ucl.ac.uk/psiout/ab6766dd548c0639.psi_2.jpg

Please cite:

Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202.

McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics. 16, 404-405.

(Note that the links above are alive for 3 days only. The URL listed will not bring anything up after August 16 2008!)

• PDF output:

File:PsipredOutputEColi.pdf

• JPG outputs:
  • Page 1
    
  • Page 2
    

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