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EMBOSS: cutseq |
It removes the sequence from the specified start to the end positions (inclusive) and returns the rest of the sequence in the output file.
% cutseq gatta.seq gatta2.seq -from=10 -to=12
To remove the first 20 bases from 'hatta.seq' and write it to 'jsh.seq':
% cutseq -seq=hatta.seq -from=1 -to=20 -out=jsh.seq
Mandatory qualifiers:
[-sequence] sequence Sequence USA
-from integer This is the start position (inclusive) of
the section of the sequence that you wish to
remove.
-to integer This is the end position (inclusive) of the
section of the sequence that you wish to
remove.
[-outseq] seqout Output sequence USA
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 | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
| -from | This is the start position (inclusive) of the section of the sequence that you wish to remove. | Any integer value | Start of sequence (0) |
| -to | This is the end position (inclusive) of the section of the sequence that you wish to remove. | Any integer value | End of sequence (0) |
| [-outseq] (Parameter 2) |
Output sequence USA | Writeable sequence | <sequence>.format |
| Optional qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced qualifiers | Allowed values | Default | |
| (none) | |||
| Program name | Description |
|---|---|
| biosed | Replace or delete sequence sections |
| degapseq | Removes gap characters from sequences |
| descseq | Alter the name or description of a sequence |
| entret | Reads and writes (returns) flatfile entries |
| extractfeat | Extract features from a sequence |
| extractseq | Extract regions from a sequence |
| 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 |
| newseq | Type in a short new 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 |
| 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 |
| 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 |