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PP Help 04: Advanced input options

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.
   

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