trimseq 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 Remove unwanted characters from start and end of sequence(s) Description trimseq reads one or more sequences and writes the same sequences out, but removing any regions at the start and / or end that contain unwanted characters. These include gap characters (where occur the sequences have been aligned), X's and N's (in nucleotide sequences), *'s (optionally) and (optionally) IUPAC ambiguity codes. Usage Here is a sample session with trimseq % trimseq untrimmed.seq trim1.seq -window 1 -percent 100 Remove unwanted characters from start and end of sequence(s) Go to the input files for this example Go to the output files for this example Example 2 % trimseq untrimmed.seq trim2.seq -window 5 -percent 40 Remove unwanted characters from start and end of sequence(s) Go to the output files for this example Example 3 % trimseq untrimmed.seq trim3.seq -window 5 -percent 50 Remove unwanted characters from start and end of sequence(s) Go to the output files for this example Example 4 % trimseq untrimmed.seq trim4.seq -window 5 -percent 50 -strict Remove unwanted characters from start and end of sequence(s) Go to the output files for this example Example 5 % trimseq untrimmed.seq trim5.seq -window 5 -percent 50 -strict -noright Remove unwanted characters from start and end of sequence(s) Go to the output files for this example Command line arguments Remove unwanted characters from start and end of sequence(s) Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall (Gapped) sequence(s) filename and optional format, or reference (input USA) [-outseq] seqoutall [.] Sequence set(s) filename and optional format (output USA) Additional (Optional) qualifiers: -window integer [1] This determines the size of the region that is considered when deciding whether the percentage of ambiguity is greater than the threshold. A value of 5 means that a region of 5 letters in the sequence is shifted along the sequence from the ends and trimming is done only if there is a greater or equal percentage of ambiguity than the threshold percentage. (Integer 1 or more) -percent float [100.0] This is the threshold of the percentage ambiguity in the window required in order to trim a sequence. (Any numeric value) -strict boolean [N] In nucleic sequences, trim off not only N's and X's, but also the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B. In protein sequences, trim off not only X's but also B and Z. -star boolean [N] In protein sequences, trim off not only X's, but also the *'s Advanced (Unprompted) qualifiers: -[no]left boolean [Y] Trim at the start -[no]right boolean [Y] Trim at the end Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each 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 Normal sequence. Input files for usage example File: untrimmed.seq >myseq ...ttyyyctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc tctaataaaaaagccacttagttca.gnntcynnnnnn Output file format Normal sequence file. Output files for usage example File: trim1.seq >myseq ttyyyctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc tctaataaaaaagccacttagttca-gnntcy Output files for usage example 2 File: trim2.seq >myseq ttyyyctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc tctaataaaaaagccacttagttca-g Output files for usage example 3 File: trim3.seq >myseq ttyyyctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc tctaataaaaaagccacttagttca-gnntcy Output files for usage example 4 File: trim4.seq >myseq ctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcagctc tttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcccag atcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgctcctg gcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccctgact accctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggcccgtgct ggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaagaagaca ggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgcccaccttt ggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttctctaa taaaaaagccacttagttca-gnntc Output files for usage example 5 File: trim5.seq >myseq ctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgcagctc tttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcccag atcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgctcctg gcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccctgact accctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggcccgtgct ggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaagaagaca ggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgcccaccttt ggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttctctaa taaaaaagccacttagttca-gnntcynnnnnn Data files None. Notes trimseq will remove from a terminal region: * all gap characters * X's and N's (in nucleic sequences) * *'s (optional) * IUPAC ambiguity codes: B and Z in proteins, M,R,W,S,Y,K,V,H,D and B in nucleic sequences (optional) Rather than removing individual characters, it removes an entire segment, using a threshold percentage of unwanted characters in a window of a specified size which is moved along the sequence from the ends. The program stops trimming when the percentage of unwanted characters in the moving window drops below the specified threshold percentage. Thus if the window size is set to 1 and the percentage threshold is 100, no further poor quality regions will be removed. If the window size is set to 5 and the percentage threshold is 40 then the sequence AAGCTNNNNATT will be trimmed to AAGCT, while AAGCTNATT or AAGCTNNNNATTT will not be trimmed as less than 40% of the last 5 characters are N's. After trimming these poor quality regions, it will again then trim off any dangling gap characters from the ends. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None noted. 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 maskseq Write a sequence with masked regions 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 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 Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None