maskseq Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Write a sequence with masked regions Description maskseq reads a sequence and writes a masked version of it to file. The sequence is masked in a specified set of regions such that characters in that region are (optionally) converted to lower case and / or (optionally) replaced with the specified mask character. Usage Here is a sample session with maskseq Mask off bases 10 to 12 from a sequence 'prot.fasta' and write to the new sequence file 'prot2.seq': % maskseq prot.fasta prot2.seq -reg=10-12 Write a sequence with masked regions 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 prot.fasta prot2.seq -reg=20-30 -mask=x Write a sequence with masked regions 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 prot.fasta prot2.seq -reg=20-23,34-45,88-90 Write a sequence with masked regions Go to the output files for this example Example 4 Change to lower-case the regions 20 to 23, 34 to 45 and 88 to 90 in 'prot.fasta': % maskseq prot.fasta prot2.seq -reg=20-23,34-45,88-90 -tolower Write a sequence with masked regions Go to the output files for this example Command line arguments Write a sequence with masked regions Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] sequence Sequence filename and optional format, or reference (input USA) -regions range [None] 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 [.] Sequence filename and optional format (output USA) Additional (Optional) qualifiers (* if not always prompted): -tolower toggle [N] The region can be 'masked' by converting the sequence characters to lower-case, some non-EMBOSS programs e.g. fasta can interpret this as a masked region. The sequence is unchanged apart from the case change. You might like to ensure that the whole sequence is in upper-case before masking the specified regions to lower-case by using the '-supper' flag. * -maskchar string ['X' for protein, 'N' for nucleic] Character to use when masking. Default is 'X' for protein sequences, 'N' for nucleic sequences. If the mask character is set to be the SPACE character or a null character, then the sequence is 'masked' by changing it to lower-case, just as with the '-lowercase' flag. (Any string from 1 to 1 characters) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of the sequence to be used -send1 integer End of the sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outseq" associated qualifiers -osformat2 string Output seq format -osextension2 string File name extension -osname2 string Base file name -osdirectory2 string Output directory -osdbname2 string Database name to add -ossingle2 boolean Separate file for each entry -oufo2 string UFO features -offormat2 string Features format -ofname2 string Features file name -ofdirectory2 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format maskseq reads in a single nucleotide or protein sequence. Input files for usage example File: prot.fasta >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: * Comment lines start with '#' in the first column. * Comment lines and blank lines are ignored. * The line may start with white-space. * There are two positive (integer) numbers per line separated by one or more space or TAB characters. * The second number must be greater or equal to the first number. * There can be optional text after the two numbers to annotate the line. * White-space before or after the text is removed. 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 __________________________________________________________________ Output file format The output is a standard EMBOSS sequence file. The results can be output in one of several styles by using the command-line qualifier -osformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq. See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats. The sequence file has the selected range masked with the specified character. Output files for usage example File: prot2.seq >FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE ACDEFGHIKXXXPQRSTVWYACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY ACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY Output files for usage example 2 File: prot2.seq >FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE ACDEFGHIKLMNPQRSTVWxxxxxxxxxxxMNPQRSTVWYACDEFGHIKLMNPQRSTVWY ACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY Output files for usage example 3 File: prot2.seq >FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE ACDEFGHIKLMNPQRSTVWXXXXEFGHIKLMNPXXXXXXXXXXXXGHIKLMNPQRSTVWY ACDEFGHIKLMNPQRSTVWYACDEFGHXXXMNPQRSTVWY Output files for usage example 4 File: prot2.seq >FASTA F00001 FASTA FORMAT PROTEIN SEQUENCE ACDEFGHIKLMNPQRSTVWyacdEFGHIKLMNPqrstvwyacdefGHIKLMNPQRSTVWY ACDEFGHIKLMNPQRSTVWYACDEFGHiklMNPQRSTVWY Data files None. Notes 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 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. There are other uses for it. For example, some non-EMBOSS programs (for example FASTA) are capable of treating lower-case regions as if they are masked. maskseq can mask a region to lower-case instead of replacing the sequence with N's or X's if you use the qualifier -tolower or use a space character as the masking character. References None. Warnings You can mask out a complete sequence. Diagnostic Error Messages Several warning messages about malformed region specifications: * Non-digit found in region ... * Unpaired start of a region found in ... * Non-digit found in region ... * The start of a pair of region positions must be smaller than the end in ... Exit status It exits with status 0, unless a region is badly constructed. Known bugs None. See also Program name Description aligncopy Reads and writes alignments aligncopypair Reads and writes pairs from alignments biosed Replace or delete sequence sections codcopy Copy and reformat a codon usage table cutseq Removes a section from a sequence degapseq Removes non-alphabetic (e.g. gap) characters from sequences descseq Alter the name or description of a sequence entret Retrieves sequence entries from flatfile databases and files extractalign Extract regions from a sequence alignment extractfeat Extract features from sequence(s) extractseq Extract regions from a sequence featcopy Reads and writes a feature table featreport Reads and writes a feature table feattext Return a feature table original text listor Write a list file of the logical OR of two sets of sequences makenucseq Create random nucleotide sequences makeprotseq Create random protein sequences maskambignuc Masks all ambiguity characters in nucleotide sequences with N maskambigprot Masks all ambiguity characters in protein sequences with X maskfeat Write a sequence with masked features newseq Create a sequence file from a typed-in sequence nohtml Remove mark-up (e.g. HTML tags) from an ASCII text file noreturn Remove carriage return from ASCII files nospace Remove whitespace from an ASCII text file notab Replace tabs with spaces in an ASCII text file notseq Write to file a subset of an input stream of sequences nthseq Write to file a single sequence from an input stream of sequences nthseqset Reads and writes (returns) one set of sequences from many pasteseq Insert one sequence into another revseq Reverse and complement a nucleotide sequence seqcount Reads and counts sequences seqret Reads and writes (returns) sequences seqretsetall Reads and writes (returns) many sets of sequences seqretsplit Reads sequences and writes them to individual files sizeseq Sort sequences by size skipredundant Remove redundant sequences from an input set skipseq Reads and writes (returns) sequences, skipping first few splitsource Split sequence(s) into original source sequences splitter Split sequence(s) into smaller sequences trimest Remove poly-A tails from nucleotide sequences trimseq Remove unwanted characters from start and end of sequence(s) trimspace Remove extra whitespace from an ASCII text file union Concatenate multiple sequences into a single sequence vectorstrip Removes vectors from the ends of nucleotide sequence(s) yank Add a sequence reference (a full USA) to a list file Author(s) Gary Williams formerly at: MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Completed 3 March 1999 Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None