Eassemble

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EASSEMBLE

FUNCTION

EAssemble is a version of GCG's old Assemble program with command line control added.

DESCRIPTION

EAssemble lets you choose as many segments as you please from existing sequences. The ranges chosen can be from either strand. EAssemble puts all of the segments together into a new sequence file.

EAssemble supports the assembly of fragments from circular molecules by letting you define a range in the sequence that extends across the end and into the beginning of a molecule. The terminal bell rings when a circular range is chosen.

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 part of a session using EAssemble to assemble a coding sequence from the file gamma.seq: 

  
  
  % eassemble
  
   EASSEMBLE uses any sequence data
  
   EASSEMBLE of what sequence ?  gamma.seq
  
   What should I call the output file (* gamma.seg *) ?
  
          Start (* 1 *) ?  2179
       End (*  11375 *) ?  2270
       Reverse (* No *) ?
  
  That range begins ATGGG and ends GGAAG.  Is this correct (* Yes *) ?
  
  That is done, now would you like to:
  
 A)dd another segment from this sequence
 G)et segments from another sequence
  
 W)rite out this assembly into a file
  
  Please choose one (* W *):  a
  
      Start (*   1   *) ?  2393
        End (* 11375 *) ?  2615
      Reverse (* No *)  ?
  
  That range begins GCTCC and ends TCAAG. Is this correct (* Yes *) ?
  
  That is done, now would you like to:
  
 A)dd another segment from this sequence
 G)et segments from another sequence
  
 W)rite out this assembly to file
  
  Please choose one (* W *):  a
  
      Start (*   1   *) ?  3502
        End (* 11375 *) ?  3630
      Reverse (* No *)  ?
  
  That range begins CTCCT and ends ACTGA.  Is this correct (* Yes *) ?
  
  That is done, now would you like to:
  
 A)dd another segment from this sequence
 G)et segments from another sequence
  
 W)rite out this assembly to file
  
  Please choose one (* W *):
  
  %

OUTPUT FILE

Here is some of the output file: 

  
  
   EASSEMBLE    September 26, 1995 16:30
  
  Symbols:     1 to: 92    from: gamma.seq        ck: 6474,  2179 to: 2270
  Symbols:    93 to: 315   from: gamma.seq        ck: 6474,  2393 to: 2615
  Symbols:   316 to: 444   from: gamma.seq        ck: 6474,  3502 to: 3630
  
  
  Length: 444  September 26, 1995 16:31  Type: N  Check: 2906  ..
  
    1  ATGGGTCATT TCACAGAGGA GGACAAGGCT ACTATCACAA GCCTGTGGGG
  
   51  CAAGGTGAAT GTGGAAGATG CTGGAGGAGA AACCCTGGGA AGGCTCCTGG
  
     ///////////////////////////////////////////////////////
  
  351  CCATTTCGGC AAAGAATTCA CCCCTGAGGT GCAGGCTTCC TGGCAGAAGA
  
  401  TGGTGACTGG AGTGGCCAGT GCCCTGTCCT CCAGATACCA CTGA

RELATED PROGRAMS

SeqEd is a general purpose, screen-oriented sequence editor. We believe that SeqEd' s Include command is a much better way to assemble sequences than by using EAssemble Reformat puts a sequence file that has been modified with a text editor into GCG sequence file format.

RESTRICTIONS

Unknown. EAssemble allows you to concatenate peptide and nucleotide sequences without complaint; however, that is an odd thing to do. Embedded comments from the input segments are lost in the output sequence.

SUGGESTIONS

SeqEd' s Include command renders EAssemble obsolete. Please contact us if you disagree.

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. 

  
  
  Minimal Syntax: % eassemble -[INfile=]gamma.seq -Default
  
  Prompted Parameters:
  
  [-OUTfile=]gamma.seg      output file name
  -MENU1=w                  menu option
  
  Local Data Files: None
  
  Optional Parameters:
  
  -BEGin1=1 -END1=100       limits for each range
  -REVerse1                 direction for each range
  [-INfile2=]gamma.seq      second input file

LOCAL DATA FILES

None.

OPTIONAL PARAMETERS

The parameters and switches listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Basic Concepts: Using Programs in the GCG User's Guide.

-BEGin=1

specifies the start of a fragment, defaults to the start of the sequence. -BEGin2=1 refers to the second input range, and so on.

-END=201

specifies the end of a fragment, defaults to the end of the sequence. -END2=1201 refers to the second input range, and so on.

-REVerse

specifies the direction of assembly, defaults to forward. -REVerse2 refers to the second input range, and so on.

-OUTfile=myname.pep

names the output file for the assembly.

-MENu1=W

gives the answer to the menu prompt.

-MENu2=W gives the answer to a second menu prompt, and so on.

-INfile2=myname.pep

names a second input sequence for the assembly.

Printed: April 22, 1996 15:52 (1162)