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EMBOSS: nthseq |
This default behaviour can be changed by using the qualifier '-ossingle' which writes many sequences into many files, each containing one sequence. It can also be changed by using the qualifier '-osf=gcg' which forces the output sequence format to be 'GCG' format - this format cannot cope with holding multiple sequences in one file and so EMBOSS writes each GCG-format sequence into its own individual file.
If, however you have the situation where you have a file containing multiple sequences and you wish to extract one of them, then this application may be useful.
This application extracts the indicated sequence from a multiple set of sequences and writes it out.
% nthseq Input sequence: embl:eclac* The number of the sequence to output [1]: 2 Output sequence [eclaca.fasta]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA -number integer The number of the sequence to output [-outseq] seqout Output sequence USA Optional qualifiers: (none) Advanced qualifiers: (none) |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
-number | The number of the sequence to output | Integer 1 or more | 1 |
[-outseq] (Parameter 2) |
Output sequence USA | Writeable sequence | <sequence>.format |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
In the example, the search will find entries ECLACA, ECLACI, ECLACY and ECLACZ in that order.
For example:
#!/usr/local/bin/perl -w if ($#ARGV !=1) { die "Usage: scriptname in out\n"; } $count=1; @list = `infoseq $ARGV[0] -auto -only -name`; while ($count <= $#list+1) { system("nthseq -auto $ARGV[0] -n $count $ARGV[1]-$count.seq"); $count++; }
Program name | Description |
---|---|
cutseq | Removes a specified section from a sequence |
descseq | Alter the name or description of a sequence |
extractseq | Extract regions from a sequence |
maskfeat | Mask off features of a sequence |
maskseq | Mask off regions of a sequence |
megamerger | Merge two large overlapping nucleic acid sequences |
merger | Merge two overlapping nucleic acid sequences |
newseq | Type in a short new sequence |
noreturn | Removes carriage return from ASCII files |
pasteseq | Insert one sequence into another |
revseq | Reverse and complement a sequence |
splitter | Split a sequence into (overlapping) smaller sequences |
trimseq | Trim ambiguous bits off the ends of sequences |
vectorstrip | Strips out DNA between a pair of vector sequences |