## 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