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newseq |
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
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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 [
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| 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 |
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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
//
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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 | Reads and writes alignments |
| aligncopypair | Reads and writes pairs from alignments |
| biosed | Replace or delete sequence sections |
| codcopy | Copy and reformat a codon usage table |
| cutseq | Removes a section from a sequence |
| degapseq | Removes non-alphabetic (e.g. gap) characters from sequences |
| descseq | Alter the name or description of a sequence |
| entret | Retrieves 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 | Reads and writes a feature table |
| featreport | Reads and writes a feature table |
| 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 | Masks all ambiguity characters in nucleotide sequences with N |
| maskambigprot | Masks 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 all 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 |
| pasteseq | Insert one sequence into another |
| revseq | Reverse and complement a nucleotide sequence |
| seqret | Reads and writes (returns) sequences |
| seqretsplit | Reads sequences and writes them to individual files |
| sizeseq | Sort sequences by size |
| skipredundant | Remove redundant sequences from an input set |
| skipseq | Reads and writes (returns) sequences, skipping first few |
| 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 | Removes vectors from the ends of nucleotide sequence(s) |
| yank | Add a sequence reference (a full USA) to a list file |