Translate translates nucleotide sequences into peptide sequences.
Translate creates a protein sequence by translating nucleic acid sequences that you specify. In addition to translating a single range of a given nucleotide sequence, it will concatenate ranges into a single assembly for translation or translate each range before assembling them. The ranges can be of any length, come from either strand of a sequence, or even from more than one sequence file. Unlike most Wisconsin Package(TM) programs, Translate lets you specify ranges as if the sequence was circular (extending past the end of the sequence and continuing at the beginning).
Translate supports the IUB-IUPAC character set for the representation of nucleotide ambiguities. See Appendix III for a list of these characters.
Here is the output file ggamma.pep:
!!AA_SEQUENCE 1.0
TRANSLATE of: gamma.seq check: 6474 from: 2179 to: 2270
and of: gamma.seq check: 6474 from: 2393 to: 2615
and of: gamma.seq check: 6474 from: 3502 to: 3630
generated symbols 1 to: 148.
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.
ggamma.pep Length: 148 October 5, 1998 12:59 Type: P Check: 6924 ..
1 MGHFTEEDKA TITSLWGKVN VEDAGGETLG RLLVVYPWTQ RFFDSFGNLS
51 SASAIMGNPK VKAHGKKVLT SLGDAIKHLD DLKGTFAQLS ELHCDKLHVD
101 PENFKLLGNV LVTVLAIHFG KEFTPEVQAS WQKMVTGVAS ALSSRYH*
Translate accepts multiple (one or more) nucleotide sequences as input. You can specify multiple sequences in a number of ways: by using a list file, for example @project.list; by using an MSF or RSF file, for example project.msf{*}; or by using a sequence specification with an asterisk (*) wildcard, for example GenEMBL:*. If Translate rejects your nucleotide sequence, turn to Appendix VI to see how to change or set the type of a sequence.
ExtractPeptide can write one or more of the translation frames from the Map program output into protein sequence files. The PepData program translates sequences in all six frames.
Unknown.
Translate allows you to translate sequences where the reading frame is interrupted. This frame-interruption commonly occurs in eukaryotic sequences containing introns. In the example above, a single codon is divided by the first intron. To accommodate frame interruption, Translate allows you to specify ranges to translate (exons) that are not an even multiple of three in length. Translate concatenates the nucleotide ranges that you define and translates them only at the moment you choose a menu item that starts with the word Translate.
If you continue after translating an assembly, you are in effect building a new assembly (gene) and concatenating the protein sequence from the new gene onto the protein sequence you have already created.
You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.