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maskseq |
Why would you wish to do this? It is common for database searches to mask out low-complexity or biased composition regions of a sequence so that spurious matches do not occur. It is just possible that you have a program that has reported such biased regions but which has not masked the sequence itself. In that case, you can use this program to do the masking.
You may find other uses for it.
Mask off bases 10 to 12 from a sequence 'prot.fasta' and write to the new sequence file 'prot2.seq':
% maskseq ../../data/prot.fasta prot2.seq -reg=10-12 Mask off regions of a sequence. |
Go to the input files for this example
Go to the output files for this example
Example 2
Mask off bases 20 to 30 from a sequence 'prot.fasta' using the character 'x' and write to the new sequence file 'prot2.seq':
% maskseq ../../data/prot.fasta prot2.seq -reg=20-30 -mask=x Mask off regions of a sequence. |
Go to the output files for this example
Example 3
Mask off the regions 20 to 23, 34 to 45 and 88 to 90 in 'prot.fasta':
% maskseq ../../data/prot.fasta prot2.seq -reg=20-23,34-45,88-90 Mask off regions of a sequence. |
Go to the output files for this example
Mandatory qualifiers: [-sequence] sequence Sequence USA -regions range Regions to mask. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99 [-outseq] seqout Output sequence USA Optional qualifiers: -maskchar string Character to use when masking. Default is 'X' for protein sequences, 'N' for nucleic sequences. Advanced qualifiers: (none) General qualifiers: -help boolean 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 USA | Readable sequence | Required |
-regions | Regions to mask. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99 | Sequence range | None |
[-outseq] (Parameter 2) |
Output sequence USA | Writeable sequence | <sequence>.format |
Optional qualifiers | Allowed values | Default | |
-maskchar | Character to use when masking. Default is 'X' for protein sequences, 'N' for nucleic sequences. | Any string is accepted | 'X' for protein, 'N' for nucleic |
Advanced qualifiers | Allowed values | Default | |
(none) |
>FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE ACDEFGHIKLMNPQRSTVWY ACDEFGHIKLMNPQRSTVWY ACDEFGHIKLMNPQRSTVWY ACDEFGHIKLMNPQRSTVWY ACDEFGHIKLMNPQRSTVWY |
You can specify a file of ranges to mask out by giving the '-regions' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-regions @myfile').
The format of the range file is:
An example range file is:
# this is my set of ranges 12 23 4 5 this is like 12-23, but smaller 67 10348 interesting region
>FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE ACDEFGHIKXXXPQRSTVWYACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY ACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY |
>FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE ACDEFGHIKLMNPQRSTVWxxxxxxxxxxxMNPQRSTVWYACDEFGHIKLMNPQRSTVWY ACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY |
>FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE ACDEFGHIKLMNPQRSTVWXXXXEFGHIKLMNPXXXXXXXXXXXXGHIKLMNPQRSTVWY ACDEFGHIKLMNPQRSTVWYACDEFGHXXXMNPQRSTVWY |
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 |
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 |
skipseq | Reads and writes (returns) sequences, skipping the first few |
splitter | Split a sequence into (overlapping) smaller sequences |
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 |
maskfeat masks parts of the input sequence that are annotated features whose feature-names match the user-specified names.