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EMBOSS: listor |
When comparing sequences to see if they are the same between two sets of sequences, no use is made of the ID name or accession number of the sequences. Only the sequences themselves are compared. The comparison of the sequences is case-independent.
The logical union is an OR operation by default. Other available operations are: AND, XOR and NOT.
The (default) logical OR of the two sets of sequences is simply the result of merging the two sets of sequences, (without listing any shared sequences twice).
A logical AND simply lists those sequences that occur in both sets of sequences.
A logical XOR lists those sequences that ONLY occur in the first set or only occur in the second set - sequences occuring in both sets are ignored (the opposite of an AND).
A logical NOT lists all those sequences in the first set except for those that also occur in the second set.
An example of the four types of logical operation performed with the two sets of sequences comprising these sequences follows. The two sets of sequences are in the files named file1 and file2. There are 2 sequences which are duplicated between these two files ('two' and 'three') and the sequences 'one' and 'four' are unique to the files 'file1' and 'file2' respectively.
>one tagctagcg >two tagctagcggctacgt >three tagctattttatgctacgtcagtgac
>two tagctagcggctacgt >three tagctattttatgctacgtcagtgac >four gcgcggcgcgcgtgcgtcgttgctggggccc
The results of the four types of logical union follows. Note that the duplicated sequences in these two files have been given the same name. This is not necessary for the operation of listor as it compares the sequences themselves, not the ID names of the sequences.
fasta::file1:one fasta::file1:two fasta::file1:three fasta::file2:four
fasta::file1:two fasta::file1:three
fasta::file1:one fasta::file2:four
fasta::file1:one
% listor file1 file1 Writes a list file of the logical OR of two sets of sequences Output file [outfile.list]:
Mandatory qualifiers: [-firstset] seqset Sequence set USA [-secondset] seqset Sequence set USA [-outlist] outfile The list of sequence names will be written to this list file Optional qualifiers: -operator menu The following logical operators combine the sequences in the following ways: OR - gives all that occur in one set or the other AND - gives only those which occur in both sets XOR - gives those which only occur in one set or the other, but not in both NOT - gives those which occur in the first set except for those that also occur in the second 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 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
[-firstset] (Parameter 1) |
Sequence set USA | Readable sequences | Required | ||||||||
[-secondset] (Parameter 2) |
Sequence set USA | Readable sequences | Required | ||||||||
[-outlist] (Parameter 3) |
The list of sequence names will be written to this list file | Output file | <sequence>.listor | ||||||||
Optional qualifiers | Allowed values | Default | |||||||||
-operator | The following logical operators combine the sequences in the following ways: OR - gives all that occur in one set or the other AND - gives only those which occur in both sets XOR - gives those which only occur in one set or the other, but not in both NOT - gives those which occur in the first set except for those that also occur in the second |
|
OR | ||||||||
Advanced qualifiers | Allowed values | Default | |||||||||
(none) |
The order that the USAs are written out is not necessarily the same as the order of either of the input sets of sequences.
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 |
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 |