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PeptideMap creates a peptide map of an amino acid sequence.
PeptideMap marks a peptide sequence at every position where a known proteolytic enzyme or reagent might cut it. You can select one or a few enzymes or let PeptideMap use the whole list.
PeptideMap is simply the program Map run with the command-line parameter -PROGRAMname=PeptideMap. (See the documentation for Map in the Program Manual for a complete description.)
Here is a session using PeptideMap to create a peptide map of gzeinaa.pep:
% peptidemap
(Linear) (Peptide) MAP of what sequence ? gzeinaa.pep
Begin (* 1 *) ?
End (* 283 *) ?
Select the enzymes: Type nothing or "*" to get all enzymes. Type "?"
for help on which enzymes are available and how to select them.
Enzyme(* * *):
What should I call the output file (* gzeinaa.map *) ?
Mapping .......
Writing ..... ..
MAP complete with:
Sequence Length: 283
Enzymes Chosen: 8
Cutsites found: 114
CPU time: 00.29
Output file(s): gzeinaa.map
%
(Linear) (Peptide) MAP of: gzeinaa.pep check: 2106 from: 1 to: 283
Corn Storage Protein Am. Ac. (19,000, genomic)
extracted from GZEIN.SEQ, checksum 2842, row a
With 8 enzymes: *
October 2, 1996 11:14 ..
Chymo ProEn
Chymo | Staph |
Chymo| | NTCB | |
Chymo|| | Chymo | | |
CnBr|| | CnBr | | |
Chymo ||| | ProEn | | | |
Chymo | ||| | Chymo | | | | |
NTCB | ||| | Chymo| | | | | |
Trypsin | | ||| | ProEn|| | | | | |
Chymo | | | ||| | ProEn||| | | | | |
Trypsin CnBr | | | ||| | NTCB Chymo |||| | | | | |
Trypsin|ProEn | | | | ||| | ProEn|ProEn | |||| | | | | |
|| | | | | | ||| | || | | |||| | | | | |
RKHNIVPIMAAKIFCLIMLLGLSASAATASIFPQCSQAPIASLLPPYLSPAMSSVCENPI
1 ---------+---------+---------+---------+---------+---------+ 60
///////////////////////////////////////////////////////////////////////
Enzymes that do cut:
Chymo CnBr NTCB ProEn Staph Trypsin
Enzymes that do not cut:
NH2OH pH2.5
PeptideMap accepts a single protein sequence as input. If PeptideMap rejects your protein sequence, turn to Appendix VI to see how to change or set the type of a sequence.
PeptideSort shows the peptide fragments from a digest of an amino acid sequence. It sorts the peptides by weight, position, and HPLC retention at pH 2.1, and shows the composition of each peptide. It also prints a summary of the composition of the whole protein.
It only makes sense to use PeptideMap on peptide sequences. See the documentation for the program Map.
See the documentation for the program Map.
See the documentation for the program Map.
The files described below supply auxiliary data to this program. The program automatically reads them from a public data directory unless you either 1) have a data file with exactly the same name in your current working directory; or 2) name a file on the command line with an expression like -DATa1=myfile.dat. For more information see Chapter 4, Using Data Files in the User's Guide.
The file proenzyme.dat contains the enzyme data.
The parameters listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
See the documentation for the program Map.
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