PEPTIDEMAP

Table of Contents

FUNCTION

DESCRIPTION

EXAMPLE

FUNCTION

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PeptideMap creates a peptide map of an amino acid sequence.

DESCRIPTION

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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 -PROGRAMname=PeptideMap. (See the documentation for Map in the Program Manual for a complete description.)

EXAMPLE

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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

OUTPUT FILE

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Here is some of the output file:

 (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 8, 1998 14:40  ..

                          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

INPUT FILES

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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.

RELATED PROGRAMS

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PeptideSort shows the peptide fragments from a digest of an amino acid sequence. It sorts the peptides by position, putative molecular weight, and relative 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.

CHOOSING THE ENZYMES

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See the documentation for the program Map for a complete description of choosing enzymes.

COMMAND-LINE SUMMARY

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All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional.

Minimal Syntax: % peptidemap [-INfile=]gzeinaa.pep -Default

Prompted Parameters:

-BEGin=1 -END=283          sets the range of interest

-ENZymes=*[,...]           selects peptidases used in the search

[-OUTfile=]gzeinaa.map     names the output file

Local Data Files:

-DATa=proenzyme.dat        specifies name and specificity of each peptidase

Optional Parameters:

-WIDth=100       sets display width to something other than 60 aa/line

-PAGe[=62]       adds form-feeds to keep clusters on a single page

-ONCe            shows peptidases that cut only once

-MINCuts=2       shows only peptidases that cut at least 2 times

-MAXCuts=2       shows only peptidases that cut no more than 2 times

-EXCLude=n1,n2   suppresses peptidases that cut between n1 and n2

-RSF[=map.rsf]   saves sites as features in RSF file

-APPend          appends the input data files to the output file

-CUTters[=fn]    writes enzyme data file with enzymes that did cut

-NONCUTters[=fn] writes enzyme data file with enzymes that did not cut

-EXCUTters[=fn]  writes enzyme data file with enzymes that were excluded

-MISmatch=1      finds cleavage sites with one or fewer mismatches

-MINCuts=2       shows only enzymes that cut at least 2 times

-MAXCuts=2       shows only enzymes that cut no more than 2 times

-ONCe            shows only enzymes that cut once

-EXCLude=n1,n2   doesn't show enzymes that cut between residues n1 and n2

-VERtical        displays peptidase name vertically over cleavage site

-NOCUTline       suppresses line of '|' characters showing cut points

-NOSEQline       suppresses the sequence display

-NOSCALeline     suppresses the scale line

-TABle           shows the map as a list of cut positions, sorted by position

  -SORtbyenzyme    sorts table output first by enzyme, then by cut position

-NOMONitor       suppresses the screen monitor

-NOSUMmary       suppresses the screen summary

LOCAL DATA FILES

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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 Section 4, Using Data Files in the User's Guide.

The file proenzyme.dat contains the enzyme data.

PARAMETER REFERENCE

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You can set the parameters listed below from the command line.

-ENZymes=*[,...]

Specifies the enzymes whose recognition sites you want to search. If you search for several different enzymes, separate their names with commas. -ENZymes=* selects all enzymes and -ENZymes=Al* selects all enzymes whose names start with Al.

-RSF=peptidemap.rsf

Writes an RSF (rich sequence format) file containing the input sequences annotated with features generated from the results of PeptideMap. This RSF file is suitable for input to other Accelrys GCG (GCG) programs that support RSF files. In particular, you can use SeqLab to view this features annotation graphically. If you don't specify a file name with this parameter, then the program creates one using peptidemap for the file basename and .rsf for the extension. For more information on RSF files, see "Using Rich Sequence Format (RSF) Files" in Section 2 of the User's Guide. Or, see "Rich Sequence Format (RSF) Files" in Appendix C of the SeqLab Guide.

-PAGe=60

Printed output from this program may cross from one page to another in an annoying way. Use this parameter to add form feeds to the output file in order to try to keep clusters of related information together. You can set the number of lines per page by supplying a number after -PAGe.

-WIDth=100

Allows you to choose the number of residues shown on each line of output. The standard is 60, which can be shown on a terminal screen nicely, but 100 sequence symbols per line is very convenient for estimating the size of fragments between cuts.

-MISmatch=1

Causes the program to recognize sites that are like the recognition site but with one or fewer mismatches. If too many mismatches are allowed, the results may not be meaningful. The output from most mapping programs distinguishes between sites with no mismatches and sites with mismatches.

-APPend

Appends the enzyme data file to your output file.

-CUTters=gamma.cutters

Writes out a new enzyme data file containing those selected enzymes that did cut your sequence and were not excluded with any of the -MINCuts, -ONCe, -MAXCuts, and -EXClude parameters. If you do not add a file name to the -CUTters parameter the output file will have the name of your sequence followed by the file name extension .cutters

-NONCUTters=gamma.noncutters

Writes out a new enzyme data file containing the selected enzymes that did NOT cut your sequence. If you do not add a file name to this parameter the output file will have the name of your sequence followed by the file name extension .noncutters

-EXCUTters=gamma.excutters

Writes out a new enzyme data file containing those enzymes that did cut your sequence but were excluded with any of the -EXClude, -MINCuts, -ONCe, and -MAXCuts parameters. If you do not add a file name to this parameter the output file will have the name of your sequence followed by the file name extension.excutters

The -MINCuts, -MAXCuts, -ONCe, and -EXClude parameters suppress the display of selected enzymes. The list of excluded enzymes in the program output includes both selected enzymes that cut within excluded ranges and selected enzymes that did not cut the right number of times.

-MINCuts=2

Excludes enzymes that do not cut at least two times.

-MAXCuts=2

Excludes enzymes that cut more than two times.

-ONCe

Excludes, from the set of enzymes displayed, those enzymes that cut your sequence more than once (equivalent to setting both mincuts and maxcuts to one).

-EXClude=n1,n2[,n3,n4,...]

Excludes enzymes that cut anywhere within one or more ranges of the sequence. If an enzyme is found within an excluded range, then the enzyme is not displayed. The list of excluded enzymes includes enzymes that cut within excluded ranges. The ranges are defined with sets of two numbers. The numbers are separated by commas. Spaces between numbers are not allowed. The numbers must be integers that fall within the sequence beginning and ending points you have chosen. The range may be circular if circular mapping is being done. Exclusion is not done if there are any non-numeric characters in the numbers or numbers out of range or if there is an odd number of integers following the parameter.

-VERtical

Shows enzyme names vertically over (or under) the position where they cut. When a collision at a cut point requires more than one enzyme to be displayed at that point, Map uses the next unoccupied column to the right. A '/' below the enzyme's name indicates that the name of the enzyme has been displaced. When the number of finds is very great, the resolution of this kind of display is inadequate. If the display seems too full, either restrict the number of enzymes chosen or use the default horizontal enzyme display.

 (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 8, 1998 14:40  ..

         TT         T

         rr         r

         yy    P C  y C C C CCC          P     P   C PPCC P C    S P

         pp    r hC p hNh hChhh          rN    r   h rrhh r hC N t r

         ss    o yn s yTy ynyyy          oT    o   y ooyy o yn T a o

         ii    E mB i mCm mBmmm          EC    E   m EEmm E mB C p E

         nn    n or n oBo orooo          nB    n   o nnoo n or B h n

         ||    | |/ | |/| |///|          ||    |   | |||| | |/ | | |

         RKHNIVPIMAAKIFCLIMLLGLSASAATASIFPQCSQAPIASLLPPYLSPAMSSVCENPI

       1 ---------+---------+---------+---------+---------+---------+ 60

 ///////////////////////////////////////////////////////////////////////

 Enzymes that do cut:

    Chymo     CnBr     NTCB    ProEn    Staph  Trypsin

 Enzymes that do not cut:

    NH2OH    pH2.5

The center of the PeptideMap display is a line showing the cut points with '|' characters, the sequence, and a scale. These parameters let you suppress any of these lines.

-NOCUTline

Suppresses the line of '|' characters between the enzyme name and the strand it cuts.

-NOSEQline

Suppresses the sequence display.

-NOSCALeline

Suppresses the scale line below the sequence.

-TABle

If you simply want a table of which enzymes cut where use this parameter. See the topic TABLE OUTPUT.

-SORtbyenzyme

Table output is normally sorted by the position of the cut in the sequence. Use this parameter to see the cuts sorted first by enzyme and then by position. See the topic TABLE OUTPUT.

-MONitor

This program normally monitors its progress on your screen. However, when you use -Default to suppress all program interaction, you also suppress the monitor. You can turn it back on with this parameter. If you are running the program in batch, the monitor will appear in the log file.

-SUMmary

Writes a summary of the program's work to the screen when you've used -Default to suppress all program interaction. A summary typically displays at the end of a program run interactively. You can suppress the summary for a program run interactively with -NOSUMmary.

You can also use this parameter to cause a summary of the program's work to be written in the log file of a program run in batch.

Printed: May 27, 2005 13:56

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