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EMBOSS: 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?)
% 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
//
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] list 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
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| 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 | ||||
| [-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) | |||||||
| 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 |
| extractseq | Extract regions from a sequence |
| infoseq | Displays some simple information about sequences |
| 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 |
| seqretall | Reads and writes (returns) a set of sequences one at a time |
| seqretset | Reads and writes (returns) a set of sequences all at once |
| 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 |
| vectorstrip | Strips out DNA between a pair of vector sequences |