Prime User Manual - ISP
Prime User Manual - ISP
Prime User Manual - ISP
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<strong>Prime</strong> <strong>User</strong> <strong>Manual</strong><br />
Appendix C: File Formats<br />
C.1 Input File Formats<br />
The input file formats are:<br />
• native (Schrödinger) format<br />
• FASTA format<br />
• PDB format<br />
Appendix C<br />
Sequences are read from the PDB SEQRES records, if they exist. Otherwise they are read<br />
from the ATOM records. If SEQRES records do not exist and residues are missing from<br />
the ATOM records, the query sequence will of course contain gaps.<br />
• NBRF-PIR format<br />
• TEXT-PLAIN format<br />
• GCG format<br />
• SWISS-PROT format<br />
• GENBANK format<br />
• NCBI format<br />
• PHYLIP format<br />
• NEXUS-PAUP format<br />
• SELEX format<br />
• STADEN format<br />
• PFAM-STOCKHOLM format<br />
• CASP format<br />
C.2 Output File Formats<br />
The output file formats are:<br />
• native (Schrödinger) format<br />
• FASTA format<br />
• NBRF-PIR format<br />
• TEXT-PLAIN format<br />
• GCG format<br />
• SWISS-PROT format<br />
• CASP format<br />
• GENBANK format<br />
<strong>Prime</strong> 2.1 <strong>User</strong> <strong>Manual</strong> 125
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