Eextractpeptide
EEXTRACTPEPTIDE
FUNCTION
EExtractPeptide is a version of ExtractPeptide with command line control. ExtractPeptide writes a peptide sequence from one or more of the translation frames displayed in the output from Map. Translate supercedes ExtractPeptide for most applications.
DESCRIPTION
You can see the peptide sequence from any of the six possible DNA reading frames by running the Map program. You may wish to look at these sequences with tools like Find, Compare, BestFit, or WordSearch. EExtractPeptide takes these sequences from the output file of Map and writes them into a new sequence file. If more than one frame of translation is chosen, then the sequences from each frame are concatenated. If any translations from the opposite strand are chosen, then the peptide sequences are reversed to maintain amino => carboxyl orientation.
Translate is a more general way to translate DNA sequences when the start and stop positions are already known.
AUTHOR
This GCG program was modified by Jaakko Hattula (Tampere University of Technology, Finland) and Peter Rice (E-mail: pmr@sanger.ac.uk Post: Informatics Division, The Sanger Centre, Hinxton Hall, Cambridge, CB10 1RQ, UK).
All EGCG programs are supported by the EGCG Support Team, who can be contacted by E-mail (egcg@embnet.org).
EXAMPLE
Here is a session using EExtractPeptide to extract the three forward reading frames from gamma.seq between bases 2101 and 2600 (the output from the example session for Map generated the file gamma.map):
% eextractpeptide
EXTRACTPEPTIDE from what MAP output file ? gamma.map
What translation frame(s) ( A - F ) (* ABC *) ?
What should I call the output file (* gamma.pep *) ? test.pep
%
OUTPUT
Here is part of the output file:
EXTRACTPEPTIDE of frames: ABC from: gendocdata:gamma.map
(Linear) MAP of: gamma.seq check: 6474 from: 2101 to: 2600
Human fetal beta globins G and A gamma
from Shen, Slightom and Smithies, Cell 26; 191-203.
Analyzed by Smithies et al. Cell 26; 345-353.
With 149 enzymes: *
Frame A from: 1 to: 167
Frame B from: 168 to: 334
Frame C from: 335 to: 500
Length: 500 March 7, 1991 19:26 Type: P Check: 3591 ..
1 RKHPSAVPHT RFWNV*GYQ* APSPDAMGHF TEEDKATITS LWGKVNVEDA
51 GGETLGR*AL VTRTREGRKD PVPGKSPGRF SGFVAPSDCQ TVLVNLTGSW
//////////////////////////////////////////////////////////
401 KEGPCAWQKS RSLLRICGTF *LSNCSCQSH RLLVVYPWTQ RFFDSFGNLS
451 SASAIMGNPK VKAHGKKVLT SLGDAIKHLD DLKGTFAQLS ELHCDKLHVD
RELATED PROGRAMS
ETranslate is a version of GCG's old Translate program with command line control added. EExtractPeptide is a version of ExtractPeptide with command line control. ExtractPeptide writes a peptide sequence from one or more of the translation frames displayed in the output from Map. Translate supercedes ExtractPeptide for most applications. AllTrans translates a set of aligned nucleotide sequences into protein. MyTrans is a simple EGCG application that translates part of a nucleotide sequence into protein.
PepStats gives a short statistical summary on the composition of a protein sequence and gives the molecular weight and isoelectric point.
RESTRICTIONS
EExtractPeptide writes its output sequence file in single-letter codes only; this is the standard for sequence files. The codes are described in Appendix III. If any reading frame is on the opposite strand, the peptide sequence from the Map output file is reversed to maintain amino=>carboxyl orientation. You could put the sequence back the way it was in the Map output file with the Reverse program.
INPUT FILE
EExtractPeptide reads the output from Map. (See the OUTPUT topic in the Program Manual entry for Map. )
COMMAND-LINE SUMMARY
All parameters for this program may be put on the command line. Use the option -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the qualifier names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose qualifiers or parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.
Minimum syntax: % eextractpeptide [-INfile=]gamma.map -Default Prompted Parameters: -FRAME=ABC Frame(s) of translation in Map file [-OUTfile=]gamma.pep Output file Optional Parameters: None
LOCAL DATA FILES
None.
OPTIONAL PARAMETERS
None.
Printed: April 22, 1996 15:52 (1162)