Alltrans

Go back to top

ALLTRANS

ALLTRANS

FUNCTION

AllTrans translates a set of aligned nucleotide sequences into protein.

DESCRIPTION

AllTrans reads a set of aligned nucleotide sequences, for example an MSF file from PileUp, and translates a range of bases into protein sequences.

No allowance is made for gaps in the nucleotide sequence alignment at present. Gaps should be in frame and in multiples of 3 to keep the protein translation correct and in alignment.

Single sequences can also be translated using AllTrans with the start and end positions specified on the command line. The optional output file specification can be set for each sequence if more than one input sequence is given.

AUTHOR

This program was written by 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 sample session with AllTrans

  
  
  % alltrans
  
   ALLTRANS uses any sequences
  
   ALLTRANS of what sequence(s) : dna.msf{*}
  
                Start (* 1 *) ? 211
               End (* 1062 *) ? 1059
  
   What should I call the output file (* p1c1.pep *) ?
  
   What should I call the output file (* p7c1.pep *) ?
  
  %

OUTPUT

The output from AllTrans is a set of protein sequences in files with the original sequence name and the extension ".pep" (in the example, the files will be called p1c1.pep and p7c1.pep).

INPUT FILE

The input file for AllTrans is a GCG MSF file or a wildcard set of sequences. AllTrans can also be used to translate a single sequence with command line control as an alternative to the GCG program Translate.

You can fetch the input file for the above example. Its name is EGenRunData:dna.msf.

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. MyTrans is a simple EGCG application that translates part of a nucleotide sequence into protein.

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: % alltrans [-INfile=]dna.msf{*} -Default
  
  Prompted Parameters:
  
  -BEGin=1
  -END=100
  
  Local Data Files:
  
  -TRANSlate=translate.txt   defines translation code to be used
  
  Optional Parameters:
  
  -OUTfile1=MyFile.Pep       specifies an output file for each sequence

LOCAL DATA FILES

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.

AllTrans uses translate.txt to make the translation. If the standard translation table does not apply to your sequence, you can provide the file translate.txt in your current default directory or name it on the command line with an expression like -TRANSlate=myscheme.txt. Translation tables are discussed in the Data Files volume of the Data Reference Set.