|   | newseq | 
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?)
Type in a short sequence to the file 'mycc.pep' in SWISSPROT format:
| 
% newseq 
Type in a short new sequence.
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
output sequence [outfile.fasta]: swiss::mycc.pep
 | 
Go to the output files for this example
| 
   Standard (Mandatory) qualifiers:
  [-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. (Any string is
                                  accepted)
  [-description]       string     Enter any description of the sequence that
                                  you require. (Any string is accepted)
  [-type]              menu       [N] Type of sequence (Values: N (Nucleic); P
                                  (Protein))
  [-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. (Any string is
                                  accepted)
  [-outseq]            seqout     [ | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |||||
|---|---|---|---|---|---|---|---|
| [-name] (Parameter 1) | 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 2) | Enter any description of the sequence that you require. | Any string is accepted | An empty string is accepted | ||||
| [-type] (Parameter 3) | Type of sequence | 
 | N | ||||
| [-sequence] (Parameter 4) | 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 | ||||
| [-outseq] (Parameter 5) | Sequence filename and optional format (output USA) | Writeable sequence | <*>.format | ||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||
| (none) | |||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||
| (none) | |||||||
| 
ID   cytoc          Unreviewed;         12 AA.
DE   fragment of cytochrome c
SQ   SEQUENCE    12 AA;   1464 MW;  6F142FA88DADC40B CRC64;
     KKKEERADLI AY
//
 | 
| Program name | Description | 
|---|---|
| biosed | Replace or delete sequence sections | 
| codcopy | Reads and writes a codon usage table | 
| 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 | 
| extractalign | Extract regions from a sequence alignment | 
| extractfeat | Extract features from a sequence | 
| extractseq | Extract regions from a sequence | 
| listor | Write a list file of the logical OR of two sets of sequences | 
| makenucseq | Creates random nucleotide sequences | 
| makeprotseq | Creates random protein sequences | 
| maskfeat | Mask off features of a sequence | 
| maskseq | Mask off regions of a sequence | 
| noreturn | Removes carriage return from ASCII files | 
| notseq | Exclude a set of sequences and write 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 | 
| skipseq | Reads and writes (returns) sequences, skipping first few | 
| splitter | Split a sequence into (overlapping) smaller sequences | 
| 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 |