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EMBOSS: splitter |
% splitter one_huge.seq many_small.seqTo split a sequence into sub-sequences of 50,000 bases with an overlap of 3,000 bases on each sub-sequence.
% splitter one_huge.seq many_small.seq -size=50000 -over=3000
Mandatory qualifiers: [-sequence] seqall Sequence database USA [-outseq] seqoutall Output sequence(s) USA Optional qualifiers: -size integer Size to split at -overlap integer Overlap between split sequences Advanced qualifiers: (none) General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
[-outseq] (Parameter 2) |
Output sequence(s) USA | Writeable sequence(s) | <sequence>.format |
Optional qualifiers | Allowed values | Default | |
-size | Size to split at | Integer 1 or more | 10000 |
-overlap | Overlap between split sequences | Integer 0 or more | 0 |
Advanced qualifiers | Allowed values | Default | |
(none) |
The names of the sequences are the same as the original sequence, with '_start-end' appended, where 'start', and 'end' are the start and end positions of the sub-sequence. eg: The name HSHBB would be changed in the sub-sequences to: HSHBB_1-50000 and HSHBB_50001-73308 if they were split at the size of 50000 with no overlap.
Program name | Description |
---|---|
biosed | Replace or delete sequence sections |
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 |
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 |
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 |