Name

Synopsis

Description

Predicates

fastaseq/3

Metadata

Source

fasta_db - prolog schema for fasta format

  :- use_module(bio(fasta_db)).
  :- use_module(bio(io)).

  demo:-
    load_biofile(fasta,'utr.fasta'),
    forall( (fastaseq(ID,_,Seq),sub_atom(Seq,Pos,_,_,'CGCATATC')),
            format('Subseq in ~w at ~w~n',[ID,Pos])).
  

fasta sequence model

sequence data can also be modeled in the seqfeature_db module - see feature_residues/2

however, the seqfeature_db module may be overkill for some applications where it is desirable to have a simple fasta style ID-header-sequence model

in addition, the seqfeature_db model requires a feature type for each feature, which is not stored in a standard way in the fasta model

View source: fasta_db.pro ( plaintext )