Bio.SeqLoc.Transcript

Type for splice junctions

newtype Junction

Splice junctions, which are isomorphic to the introns they span, but which support other biologically relevant constructors and accessors.

Constructors

Junction

Fields

intron :: ContigLoc

Instances

Show Junction

LocRepr Junction

fromDonorAcceptor :: Pos -> Pos -> Junction

Create a splice junction from a donor position (the last position in the 5' exon) and the acceptor position (the first position in the 3' exon).

donor :: Junction -> Pos

Donor position, i.e., the last position in the 5' exon around a junction.

acceptor :: Junction -> Pos

Acceptor position, i.e., the first position in the 3' exon around a junction.

junctions :: SpliceLoc -> [Junction]

List of splice junctions from a spliced location, in order.

Representation of transcript

data Transcript

Representation of a genomic transcript, with a gene and a transcript identifier, along with the genomic location of the processed transcript and an optional coding sequence on that transcript.

Constructors

Transcript

Fields

geneId :: !SeqName

Gene or locus name for a collection of transcripts

trxId :: !SeqName

Specific transcript identifier

location :: !SpliceSeqLoc

Sequence location of processed transcript

cds :: !(Maybe ContigLoc)

Location of CDS on the transcript

Instances

Show Transcript

utr5 :: Transcript -> Maybe ContigLoc

Just the location of the 5' UTR on the transcript, or Nothing if there is no cds on the transcript or if the cds location begins at the first nucleotide of the transcript--if a region is returned it will have positive length.

utr3 :: Transcript -> Maybe ContigLoc

Just the location of the 3' UTR on the transcript, or Nothing if there is no cds on the transcript or if the cds location ends at the last nucleotide of the transcript--if a region is returned it will have positive length.

cdsLocation :: Transcript -> Maybe SpliceSeqLoc

Genomic location of CDS within the transcript

sortContigs :: [ContigLoc] -> Maybe [ContigLoc]

Just the input contigs sorted in stranded order, when all lie on the same strand, or Nothing if they are not all on the same strand.