
                                    mse 



Function

   Multiple Sequence Editor

Description

   This is a port of Will Gilbert's MSE multiple sequence editor from the
   original C code.

Algorithm

Usage

   Here is a sample session with mse


% mse dna.msf msf::mse.msf 
Multiple Sequence Editor

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     File containing a sequence alignment
  [-outseq]            seqoutset  [.] Sequence set filename
                                  and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outseq" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

Input file format

   mse reads any normal sequence USAs.

  Input files for usage example

  File: dna.msf

!!NA_MULTIPLE_ALIGNMENT

 dna.msf  MSF: 120  Type: N  January 01, 1776  12:00  Check: 3196 ..

 Name: MSFM1          Len:   120  Check:  8587  Weight:  1.00
 Name: MSFM2          Len:   120  Check:  6178  Weight:  1.00
 Name: MSFM3          Len:   120  Check:  8431  Weight:  1.00

//

        MSFM1  ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC
        MSFM2  ACGTACGTAC GTACGTACGT ....ACGTAC GTACGTACGT ACGTACGTAC
        MSFM3  ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT CGTACGTACG

        MSFM1  GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT
        MSFM2  GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT
        MSFM3  TACGTACGTA CGTACGTACG TACGTACGTA ACGTACGTAC GTACGTACGT

        MSFM1  ACGTACGTAC GTACGTACGT
        MSFM2  ACGTACGTTG CAACGTACGT
        MSFM3  ACGTACGTAC GTACGTACGT

Output file format

   mse outputs a graph to the specified graphics device. outputs a report
   format file. The default format is ...

  Output files for usage example

  File: mse.msf

!!NA_MULTIPLE_ALIGNMENT 1.0

  mse.msf MSF: 120 Type: N 15/07/07 CompCheck: 2784 ..

  Name: MSFM1      Len: 120  Check: 8587 Weight: 1.00
  Name: MSFM2      Len: 120  Check: 5766 Weight: 1.00
  Name: MSFM3      Len: 120  Check: 8431 Weight: 1.00

//

           1                                               50
MSFM1      ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC
MSFM2      ACGTACGTACGTACGTACGTacgt....ACGTACGTACGTACGTACGTAC
MSFM3      ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTCGTACGTACG

           51                                             100
MSFM1      GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
MSFM2      GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
MSFM3      TACGTACGTACGTACGTACGTACGTACGTAACGTACGTACGTACGTACGT

           101              120
MSFM1      ACGTACGTACGTACGTACGT
MSFM2      ACGTACGTTGCAACGTACGT
MSFM3      ACGTACGTACGTACGTACGT

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                        Description
   edialign     Local multiple alignment of sequences
   emma         Multiple alignment program - interface to ClustalW program
   infoalign    Information on a multiple sequence alignment
   plotcon      Plot quality of conservation of a sequence alignment
   prettyplot   Displays aligned sequences, with colouring and boxing
   showalign    Displays a multiple sequence alignment
   tranalign    Align nucleic coding regions given the aligned proteins

Author(s)

   This program is an EMBOSS conversion of a program written by Will
   Gilbert as part of his MSE package.

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.
