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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
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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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| 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 |