|   | newseq | 
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newseq creates a sequence file from a sequence that is manually typed in at the command-line. This is a quicker, easier and less error-prone method than editing such a file in a text editor.
Type in a short sequence to the file 'mycc.pep' in SWISSPROT format:
| 
% newseq 
Create a sequence file from a typed-in 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
| 
Create a sequence file from a typed-in sequence
Version: EMBOSS:6.6.0.0
   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)
  [-description]       string     Enter any description of the sequence that
                                  you require. (Any string)
  [-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)
  [-outseq]            seqout     [ | 
| Qualifier | Type | Description | Allowed values | Default | ||||
|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||
| [-name] (Parameter 1) | 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 | |||||
| [-description] (Parameter 2) | string | Enter any description of the sequence that you require. | Any string | |||||
| [-type] (Parameter 3) | list | Type of sequence | 
 | N | ||||
| [-sequence] (Parameter 4) | 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 | |||||
| [-outseq] (Parameter 5) | seqout | Sequence filename and optional format (output USA) | Writeable sequence | <*>.format | ||||
| Additional (Optional) qualifiers | ||||||||
| (none) | ||||||||
| Advanced (Unprompted) qualifiers | ||||||||
| (none) | ||||||||
| Associated qualifiers | ||||||||
| "-outseq" associated seqout qualifiers | ||||||||
| -osformat5 -osformat_outseq | string | Output seq format | Any string | |||||
| -osextension5 -osextension_outseq | string | File name extension | Any string | |||||
| -osname5 -osname_outseq | string | Base file name | Any string | |||||
| -osdirectory5 -osdirectory_outseq | string | Output directory | Any string | |||||
| -osdbname5 -osdbname_outseq | string | Database name to add | Any string | |||||
| -ossingle5 -ossingle_outseq | boolean | Separate file for each entry | Boolean value Yes/No | N | ||||
| -oufo5 -oufo_outseq | string | UFO features | Any string | |||||
| -offormat5 -offormat_outseq | string | Features format | Any string | |||||
| -ofname5 -ofname_outseq | string | Features file name | Any string | |||||
| -ofdirectory5 -ofdirectory_outseq | string | Output directory | Any string | |||||
| General qualifiers | ||||||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||
| -error | boolean | Report errors | Boolean value Yes/No | Y | ||||
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | ||||
| 
ID   cytoc                   Unreviewed;          12 AA.
DE   fragment of cytochrome c
SQ   SEQUENCE   12 AA;  1464 MW;  6F142FA88DADC40B CRC64;
     KKKEERADLI AY
//
 | 
There will be a maximum permissible length (typically 255 characters) of the sequence that may be entered. This is not a property of the EMBOSS package but of the computer system you are using. Whenever you type something in at the command-line, the text is stored in a buffer before being passed to the program. There is often a limit of less than 255 characters on the size of the buffer and so also the size of the sequence you can specify to newseq. The computer will normally issue a beep when the end of buffer is reached, and allow no more character input.
| Program name | Description | 
|---|---|
| aligncopy | Read and write alignments | 
| aligncopypair | Read and write pairs from alignments | 
| biosed | Replace or delete sequence sections | 
| codcopy | Copy and reformat a codon usage table | 
| cutseq | Remove a section from a sequence | 
| degapseq | Remove non-alphabetic (e.g. gap) characters from sequences | 
| descseq | Alter the name or description of a sequence | 
| entret | Retrieve sequence entries from flatfile databases and files | 
| extractalign | Extract regions from a sequence alignment | 
| extractfeat | Extract features from sequence(s) | 
| extractseq | Extract regions from a sequence | 
| featcopy | Read and write a feature table | 
| featmerge | Merge two overlapping feature tables | 
| featreport | Read and write a feature table | 
| feattext | Return a feature table original text | 
| listor | Write a list file of the logical OR of two sets of sequences | 
| makenucseq | Create random nucleotide sequences | 
| makeprotseq | Create random protein sequences | 
| maskambignuc | Mask all ambiguity characters in nucleotide sequences with N | 
| maskambigprot | Mask all ambiguity characters in protein sequences with X | 
| maskfeat | Write a sequence with masked features | 
| maskseq | Write a sequence with masked regions | 
| nohtml | Remove mark-up (e.g. HTML tags) from an ASCII text file | 
| noreturn | Remove carriage return from ASCII files | 
| nospace | Remove whitespace from an ASCII text file | 
| notab | Replace tabs with spaces in an ASCII text file | 
| notseq | Write to file a subset of an input stream of sequences | 
| nthseq | Write to file a single sequence from an input stream of sequences | 
| nthseqset | Read and write (return) one set of sequences from many | 
| pasteseq | Insert one sequence into another | 
| revseq | Reverse and complement a nucleotide sequence | 
| seqcount | Read and count sequences | 
| seqret | Read and write (return) sequences | 
| seqretsetall | Read and write (return) many sets of sequences | 
| seqretsplit | Read sequences and write them to individual files | 
| sizeseq | Sort sequences by size | 
| skipredundant | Remove redundant sequences from an input set | 
| skipseq | Read and write (return) sequences, skipping first few | 
| splitsource | Split sequence(s) into original source sequences | 
| splitter | Split sequence(s) into smaller sequences | 
| trimest | Remove poly-A tails from nucleotide sequences | 
| trimseq | Remove unwanted characters from start and end of sequence(s) | 
| trimspace | Remove extra whitespace from an ASCII text file | 
| union | Concatenate multiple sequences into a single sequence | 
| vectorstrip | Remove vectors from the ends of nucleotide sequence(s) | 
| yank | Add a sequence reference (a full USA) to a list file | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.