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ExtractPeptide writes a peptide sequence from one or more of the translation frames displayed in the output from Map. Translate supersedes ExtractPeptide for most applications.
You can see the protein sequence from any of the six possible DNA reading frame translations by running the Map program. You may wish to analyze these protein sequences with other Wisconsin Package programs. ExtractPeptide 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 reverse strand are chosen, then the protein sequences are reversed to maintain the standard amino=>carboxyl orientation.
Translate is a more general way to translate DNA sequences when the start and stop positions are already known.
Here is a session using ExtractPeptide to extract the the three forward reading frames of the sequence gamma.seq between bases 2161 and 2600 from the the file gamma.map that was created in the example session for the Map program.
% extractpeptide 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 %
Here is part of the output file:
!!AA_SEQUENCE 1.0
EXTRACTPEPTIDE of frames: ABC from: gamma.map
(Linear) MAP of: gamma.seq check: 6474 from: 2161 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 216 enzymes: *
Frame A from: 1 to: 146
Frame B from: 147 to: 292
Frame C from: 293 to: 438
test.pep Length: 438 September 30, 1998 16:05 Type: P Check: 5036 ..
1 APSPDAMGHF TEEDKATITS LWGKVNVEDA GGETLGR*AL VTRTREGRKD
51 PVPGKSPGRF SGFVAPSDCQ TVLVNLTGSW LSTHGPRGSL TALATCPLPL
///////////////////////////////////////////////////////////
351 LLRICGTF*L SNCSCQSHRL LVVYPWTQRF FDSFGNLSSA SAIMGNPKVK
401 AHGKKVLTSL GDAIKHLDDL KGTFAQLSEL HCDKLHVD
ExtractPeptide accepts the output file created by the Map program as input. (See the OUTPUT topic in the Program Manual entry for the Map program.)
Translate is a more general way to translate DNA sequences in which the boundaries of the coding regions are known. PepData can translate nucleic acid sequences in all six reading frames.
ExtractPeptide writes the output sequence in the standard, single-letter amino acid codes described in Appendix III. If any reading frame is on the opposite strand, the protein sequence from the Map output file is reversed to maintain the standard amino=>carboxyl orientation. You could put the sequence back the way it was in the Map output file with the Reverse program.
Complete command-line control is not available for this program.
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