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An explanation of the fields and options in the CHOP submission page:
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| Sequence format |
Default: simple sequence or fasta formatted sequence
SWISS-PROT ID: Identifier from SWISS-PROT database, usually in the format of NAME_ORGANISM
More format options coming soon.. (PDB, TrEMBL, ...) |
| Output format |
TEXT: standard TXT (ASCII) format that can be displayed in any text editor
HTML:pretty output optimized for web browsers |
| BLAST E-value |
The e-value threshold when the query is searched against PrISM domains or SWISS-PROT database using BLAST, default=0.01 |
| HMMER E-value |
The e-value threshold when the query is searched against Pfam-A database using HMMER, default=0.01 |
| Min domain coverage |
CHOP requires the homologous region between the query protein and the known domain in the database to cover at least certain percentage of the known domain, default=80 |
| Min length of domain |
The minimum length of the fragment CHOP considers and reports as a domain, we recommend the value to be larger than 30 |
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If you find CHOP useful for your research, please cite:
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Liu J & Rost B (2004) CHOP proteins into structural domain-like fragments. Proteins, 55(3):678-688 MEDLINE Paper text
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Liu J & Rost B (2004) CHOP: Domain Dissection Based on Homology Nucleic Acids Research submitted.
CHOP CUBIC Contact
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