Bio::Seq::EncodedSeq - subtype of Bio::LocatableSeq to store DNA that encodes a protein $obj = new Bio::Seq::EncodedSeq(-seq => $dna, -encoding => "CCCCCCCIIIIICCCCC", -start => 1, -strand => 1, -length => 17); # splice out (and possibly revcomp) the coding sequence $cds = obj->cds; # obtain the protein translation of the sequence $prot = $obj->translate; # other access/inspection routines as with Bio::LocatableSeq and # Bio::SeqI; note that coordinates are relative only to the DNA # sequence, not it's implicit encoded protein sequence. Bio::Seq::EncodedSeq is a Bio::LocatableSeq object that holds a DNA sequence as well as information about the coding potential of that DNA sequence. It is meant to be useful in an alignment context, where the DNA may contain frameshifts, gaps and/or introns, or in describing the transcript of a gene. An EncodedSeq provides the ability to access the "spliced" coding sequence, meaning that all introns and gaps are removed, and any frameshifts are adjusted to provide a "clean" CDS. In order to make simultaneous use of either the DNA or the implicit encoded protein sequence coordinates, please see Bio::Coordinate::EncodingPair. We use the term "encoding" here to refer to the series of symbols that we use to identify which residues of a DNA sequence are protein-coding (i.e. part of a codon), intronic, part of a 5' or 3', frameshift "mutations", etc. From this information, a Bio::Seq::EncodedSeq is able to "figure out" its translational CDS. There are two sets of coding characters, one termed "implicit" and one termed "explicit". The "implicit" encoding is a bit simpler than the "explicit" encoding: 'C' is used for any nucleotide that's part of a codon, 'U' for any UTR, etc. The full list is shown below: Code Meaning ---- ------- C coding I intronic U untranslated G gapped (for use in alignments) F a "forward", +1 frameshift B a "backward", -1 frameshift The "explicit" encoding is just an expansion of the "implicit" encoding, to denote phase: Code Meaning ---- ------- C coding, 1st codon position D coding, 2nd codon position E coding, 3rd codon position I intronic, phase 0 (relative to intron begin) J intronic, phase 1 K intronic, phase 2 U untranslated 3'UTR V untranslated 5'UTR G gapped (for use in alignments) F a "forward", +1 frameshift B a "backward", -1 frameshift Note that the explicit coding is meant to provide easy access to position/phase specific nucleotides: $obj = new Bio::Seq::EncodedSeq (-seq => "ACAATCAGACTACG...", -encoding => "CCCCCCIII..." ); # fetch arrays of nucleotides at each codon position: my @pos1 = $obj->dnaseq(encoding => 'C', explicit => 1); my @pos2 = $obj->dnaseq(encoding => 'D'); my @pos3 = $obj->dnaseq(encoding => 'E'); # fetch arrays of "3-1" codon dinucleotides, useful for genomic # signature analyses without compounding influences of codon bias: my @pairs = $obj->dnaseq(encoding => 'EC');

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://www.bioperl.org/MailList.html - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email amackey@virginia.edu The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : $obj = Bio::Seq::EncodedSeq->new(-seq => "AGTACGTGTCATG", -encoding => "CCCCCCFCCCCCC", -id => "myseq", -start => 1, -end => 13, -strand => 1 ); Function: creates a new Bio::Seq::EncodedSeq object from a supplied DNA sequence Returns : a new Bio::Seq::EncodedSeq object Args : seq - primary nucleotide sequence used to encode the protein; note that any positions involved in a gap ('G') or backward frameshift ('B') should have one or more gap characters; if the encoding specifies G or B, but no (or not enough) gap characters exist, *they'll be added*; similary, if there are gap characters without a corresponding G or B encoding, G's will be inserted into the encoding. This allows some flexibility in specifying your sequence and coding without having to calculate a lot of the encoding for yourself. encoding - a string of characters (see Encoding Table) describing backwards frameshifts implied by the encoding but not present in the sequence will be added (as '-'s) to the sequence. If not supplied, it will be assumed that all positions are coding (C). Encoding may include either implicit phase encoding characters (i.e. "CCC") and/or explicit encoding characters (i.e. "CDE"). Additionally, prefixed numbers may be used to denote repetition (i.e. "27C3I28C"). Alternatively, encoding may be a hashref datastructure, with encoding characters as keys and Bio::LocationI objects (or arrayrefs of Bio::LocationI objects) as values, e.g.: { C => [ Bio::Location::Simple->new(1,9), Bio::Location::Simple->new(11,13) ], F => Bio::Location::Simple->new(10,10), } # same as "CCCCCCCCCFCCC" Note that if the location ranges overlap, the behavior of the encoding will be undefined (well, it will be defined, but only according to the order in which the hash keys are read, which is basically undefined ... just don't do that). id, start, end, strand - as with Bio::LocatableSeq; note that the coordinates are relative to the encoding DNA sequence, not the implicit protein sequence. If strand is reversed, then the encoding is assumed to be relative to the reverse strand as well.

encoding
Title : encoding Usage : $obj->encoding("CCCCCC"); $obj->encoding( -encoding => { I => $location } ); $enc = $obj->encoding(-explicit => 1); $enc = $obj->encoding("CCCCCC", -explicit => 1); $enc = $obj->encoding(-location => $location, -explicit => 1, -absolute => 1 ); Function: get/set the objects encoding, either globally or by location(s). Returns : the (possibly new) encoding string. Args : encoding - see the encoding argument to the new() function. explicit - whether or not to return explicit phase information in the coding (i.e. "CCC" becomes "CDE", "III" becomes "IJK", etc); defaults to 0. location - optional; location to get/set the encoding. Defaults to the entire sequence. absolute - whether or not the locational elements (either in the encoding hashref or the location argument) are relative to the absolute start/end of the Bio::LocatableSeq, or to the internal, relative coordinate system (beginning at 1); defaults to 0 (i.e. relative)

cds
Title : cds Usage : $cds = $obj->cds(-nogaps => 1); Function: obtain the "spliced" DNA sequence, by removing any nucleotides that participate in an UTR, forward frameshift or intron, and replacing any unknown nucleotide implied by a backward frameshift or gap with N's. Returns : a Bio::Seq::EncodedSeq object, with an encoding consisting only of "CCCC..". Args : nogaps - strip any gap characters (resulting from 'G' or 'B' encodings), rather than replacing them with N's.

translate
Title : translate Usage : $prot = $obj->translate(@args); Function: obtain the protein sequence encoded by the underlying DNA sequence; same as $obj->cds()->translate(@args). Returns : a Bio::PrimarySeq object. Args : same as the translate() function of Bio::PrimarySeqI

protseq
Title : seq Usage : $protseq = $obj->protseq(); Function: obtain the raw protein sequence encoded by the underlying DNA sequence; This is the same as calling $obj->translate()->seq(); Returns : a string of single-letter amino acid codes Args : same as the seq() function of Bio::PrimarySeq; note that this function may not be used to set the protein sequence; see the dnaseq() function for that.

dnaseq
Title : dnaseq Usage : $dnaseq = $obj->dnaseq(); $obj->dnaseq("ACGTGTCGT", "CCCCCCCCC"); $obj->dnaseq(-seq => "ATG", -encoding => "CCC", -location => $loc ); @introns = $obj->$dnaseq(-encoding => 'I') Function: get/set the underlying DNA sequence; will overwrite any current DNA and/or encoding information present. Returns : a string of single-letter nucleotide codes, including any gaps implied by the encoding. Args : seq - the DNA sequence to be used as a replacement encoding - the encoding of the DNA sequence (see the new() constructor); defaults to all 'C' if setting a new DNA sequence. If no new DNA sequence is being provided, then the encoding is used as a "filter" for which to return fragments of non-overlapping DNA that match the encoding. location - optional, the location of the DNA sequence to get/set; defaults to the entire sequence.