BioJava:CookBook:Core:Sequences

From BioJava

is is fairly straightforward to create sequences. Take a look at these examples:

Sequence objects can be created by providing a string representation as an input to the constructor:

ProteinSequence seq = new ProteinSequence("MSTNPKPQRKTKRNTNRRPQDVKFPGG");

Fetch a protein sequence based on a UniProt accession code from UniProt.

String uniProtID = "P26663";
 
// we will tell the UniProt proxy class that we are expecting a sequence that is an amino acid
AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
 
// now load the sequence from the UniProt website
UniprotProxySequenceReader<AminoAcidCompound> uniprotSequence = new UniprotProxySequenceReader<AminoAcidCompound>(uniProtID,set);
 
// and make a protein sequence out of it
ProteinSequence seq = new ProteinSequence(uniprotSequence);