PEPNET : Displays proteins as a helical net (EMBOSS)
Some explanations about the options
input Section- enter either the name of a file or the actual data
- if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button)
- OR you can type your data in the next area, or cut and paste it from another application.
- (but not both)
output Section- Prompt for amphipathic residue marking (-amphipathic)
- If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified using the qualifiers '-squares', '-diamonds' and '-octags'.
- Mark as squares (-squares)
- By default the aliphatic residues ILVM are marked with squares.
- Mark as diamonds (-diamonds)
- By default the residues DENQST are marked with diamonds.
- Mark as octagons (-octags)
- By default the positively charged residues HKR are marked with octagons.
- Display as data (-data)
- Output the data to a file instead of plotting it
- Sequence format
- The sequence will be automatically converted in the format needed for the program
- providing you enter a sequence either:
- in plain (raw) sequence format or in one of the following known formats:
- IG,GenBank,NBRF,EMBL,GCG,DNAStrider,Fitch,fasta,Phylip,PIR,MSF,ASN,PAUP,CLUSTALW
- You may enter in the text area a database entry code, or an accession number, in this form:
database:entry_name
or:database:accession.- enter either the name of a file or the actual data
Pise form generator version: 5.a (16 Dec 2002 11:54)
