Previous - Next - Bottom - PP home - PP help TOC

PP Help 04: Advanced input options

Contents

Advanced input options

  1. SWISSPROT identifier
  2. FASTA list (unaligned)
  3. PIR list (unaligned)
  4. SAF formatted alignment
  5. MSF formatted alignment
  6. FASTA list (aligned)
  7. PIR list (aligned)
  8. Column formatted prediction



ADVANCED INPUT OPTIONS (FORMATS)

The following input options have been implemented:

  1. Use a SWISSPROT identifier ('# SWISSPROT identifier')
    If you provide a valid SWISSPROT identifier (e.g. paho_chick), PP will use the respective sequence for prediction.
    Example for email submission format.
  2. Use your unaligned set of sequences ('# FASTA list')
    You can provide sequences that are not yet in the Swissprot database. The sequences will be aligned automatically by the program MaxHom; the prediction will be based on this alignment. You use the header as described before, with "# FASTA list" instead of "# sequence name". Then you append all your sequences successively in the PIR format after this line.
    Example for email submission format.
  3. Use your unaligned set of sequences ('# PIR list')
    You can provide sequences that are not yet in the Swissprot database. The sequences will be aligned automatically by the program MaxHom; the prediction will be based on this alignment. You use the header as described before, with "# PIR list" instead of "# sequence name". Then you append all your sequences successively in the PIR format after this line.
    Example for email submission format.
  4. Use your SAF alignment ('# SAF')
    You can provide your alignment input to the PHD predictions. To do so, you have to generate a file in SAF (simple alignment format). Then you append this file to the same header as described before, with "# SAF" instead of "# sequence name".
    Example for email submission format.
  5. Use your MSF alignment ('# MSF')
    You can provide your alignment input to the PHD predictions. To do so, you have to generate a file in MSF (multiple sequence format), e.g., generated by the program PILEUP (GCG). Then you append this file to the same header as described before, with "# MSF" instead of "# sequence name".
    Example for email submission format.
  6. Use your FASTA alignment ('# FASTA list')
    You can submit your alignment in FASTA format. This requires two keywords: (1) the string "# FASTA list" prompts the system to interpret your alignment as one in the FASTA format (specification and example for FASTA list format), and (2) the keyword "do NOT align" in a line before the one starting with a hash ('#'), assures that your alignment will not be re-aligned (as for the options of submitting your sequences via FASTA format).
    Example for email submission format.
  7. Use your PIR alignment ('# PIR list')
    You can submit your alignment in PIR format. This requires two keywords: (1) the string "# PIR list" prompts the system to interpret your alignment as one in the PIR format (specification and example for PIR list format), and (2) the keyword "do NOT align" in a line before the one starting with a hash ('#'), assures that your alignment will not be re-aligned (as for the options of submitting your sequences via PIR format).
    Example for email submission format.
  8. Use your prediction of 1D structure for threading ('# COLUMN format')
    You can provide your prediction of secondary structure and relative accessibility. (Both predictions are required. If you don't have, e.g., a prediction of accessibility, use PHDacc to generate it.) Your prediction will be used for threading. You use the header as described before, with "# COLUMN format" instead of "# sequence name". Then you append your prediction in the "COLUMN format" after this line.
    Example for email submission format.




Previous - Next - Top - PP home - PP help TOC