
                               EMBOSS: newseq
     _________________________________________________________________
   
                                Program newseq
                                       
Function

   Type in a short new sequence
   
Description

   This allows you to type a sequence into a file in a quick and easy
   manner.
   
   The length of the sequence you can type in is restricted to a fairly
   short length (typically less than 255 characters). This length
   restriction is not a property of the EMBOSS package, but of the
   computer system you are using. This is because, as you type in
   response to a prompt from this program, what you type is stored in the
   computer operating system before being handed over to the program.
   There is often a limit of less than 255 characters on the length of a
   response that a computer system will allow you to give.
   
   Despite this restriction, it is expected that this program will be a
   useful and easy way of constructing new sequence files.
   
   (You wouldn't want to type a long sequence in by hand, anyway, would
   you?)
   
Usage

   Type in a short sequence to the file 'mycc.pep' in EMBL format:
   
% newseq
Type in a short new sequence.
Output sequence [outfile.fasta]: embl::mycc.pep
Name of the sequence: cytoc
Description of the sequence: fragment of cytochrome C
Type of sequence

         N : Nucleic
         P : Protein
Type of sequence [N]: p
Enter the sequence: KKKEERADLIAY

   Display the resulting new file:
   
% more mycc.pep
ID   cytoc          STANDARD;      PRT;    12 AA.
DE   fragment of cytochrome C
SQ   SEQUENCE    12 AA;   1464 MW;  2BF1DB53 CRC32;
     KKKEERADLI AY
//

Command line arguments

   Mandatory qualifiers:
  [-outseq]            seqout     Output sequence USA
  [-name]              string     The name of of the sequence should be a
                                  single word that you will use to identify
                                  the sequence. It should have no (or few)
                                  punctuation characters in it.
  [-description]       string     Enter any description of the sequence that
                                  you require.
  [-type]              menu       Type of sequence
  [-sequence]          string     The sequence itself.
                                  Because of the limitation of the operating
                                  system, you will only be able to type in a
                                  short sequence of (typically) 250
                                  characters, or so.
                                  The keyboard will beep at you when you have
                                  reached this limit and you will not be able
                                  to press the RETURN/ENTER key until you have
                                  deleted a few characters.

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-outseq]
   (Parameter 1) Output sequence USA Writeable sequence <sequence>.format
   [-name]
   (Parameter 2) The name of of the sequence should be a single word that
   you will use to identify the sequence. It should have no (or few)
   punctuation characters in it. Any string is accepted An empty string
   is accepted
   [-description]
   (Parameter 3) Enter any description of the sequence that you require.
   Any string is accepted An empty string is accepted
   [-type]
   (Parameter 4) Type of sequence
   N (Nucleic)
   P (Protein)
   N
   [-sequence]
   (Parameter 5) The sequence itself. Because of the limitation of the
   operating system, you will only be able to type in a short sequence of
   (typically) 250 characters, or so. The keyboard will beep at you when
   you have reached this limit and you will not be able to press the
   RETURN/ENTER key until you have deleted a few characters. Any string
   is accepted An empty string is accepted
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   None.
   
Output file format

   Normal sequence.
   
Data files

   None.
   
Notes

   The length of the sequence you can type in is restricted to a fairly
   short length (typically less than 255 characters). If your computer
   beeps at you, you will typically have to delete the last character you
   typed and press the RETURN key.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None.
   
See also

   Program name                          Description
   biosed       Replace or delete sequence sections
   cutseq       Removes a specified section from a sequence
   degapseq     Removes gap characters from sequences
   descseq      Alter the name or description of a sequence
   entret       Reads and writes (returns) flatfile entries
   extractfeat  Extract features from a sequence
   extractseq   Extract regions from a sequence
   listor       Writes a list file of the logical OR of two sets of sequences
   maskfeat     Mask off features of a sequence
   maskseq      Mask off regions of a sequence
   noreturn     Removes carriage return from ASCII files
   notseq       Excludes a set of sequences and writes out the remaining ones
   nthseq       Writes one sequence from a multiple set of sequences
   pasteseq     Insert one sequence into another
   revseq       Reverse and complement a sequence
   seqret       Reads and writes (returns) sequences
   seqretsplit  Reads and writes (returns) sequences in individual files
   splitter     Split a sequence into (overlapping) smaller sequences
   swissparse   Retrieves sequences from swissprot using keyword search
   trimest      Trim poly-A tails off EST sequences
   trimseq      Trim ambiguous bits off the ends of sequences
   union        Reads sequence fragments and builds one sequence
   vectorstrip  Strips out DNA between a pair of vector sequences
   yank         Reads a sequence range, appends the full USA to a list file
   
Author(s)

   This application was written by Gary Williams
   (gwilliam@hgmp.mrc.ac.uk)
   
History

   Written (1999) - Gary Williams
   
Target users

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