Biobase.Infernal.RfamFasta

The Rfam.fasta.gz file provides useful information: (1) conversion between Rfam accession and Rfam identifier, (2) species accession, (3) name of said species, and (4) the sequence fasta file.

Documentation

data RfamFasta

Rfam FASTA entry.

Constructors

RfamFasta

Fields

modelAccession :: !ModelAccession

Rfam accession number RFxxxxx (the xxxxx part).

modelIdentifier :: !ModelIdentification

Rfam identifier (like 5S_rRNA).

sequenceAccession :: !EmblAccession

EMBL sequence accession identifier and position.

speciesAccession :: !SpeciesAccession

Rfam species accession.

speciesName :: !SpeciesName

Species name.

fastaData :: !StrictSeqData

FASTA data

Instances

Show RfamFasta

BioSeq RfamFasta

Since RfamFasta entries are just fasta entries...

Some in-memory lookup systems.

type ModelAC2ID = Map ModelAccession ModelIdentification

Model accession to model identifier

type ModelID2AC = Map ModelIdentification ModelAccession

Model identifier to model accession

type ACAC2RfamFasta = Map ModelAccession (Map EmblAccession RfamFasta)

Model accession and sequence accession to RfamFasta entry (and model accession to all entries for this accession).

type IDAC2RfamFasta = Map ModelIdentification (Map EmblAccession RfamFasta)

Model identifier and sequence accession to RfamFasta entry.