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Bioinformatics

The biojava manager

BioJava is a library oriented at dna, rna, and protein sequences [1,2]. With this manager we can create data models for sequences, such as a dna sequence from fasta string:

dna = biojava.DNAsFromString("> foo\nGCAT")

Or from just a sequence string, with or without a name:

Script code/DNAfromPlainSequence.groovy

dna = biojava.DNAfromPlainSequence("GCAT")
dna = biojava.DNAfromPlainSequence(
  "GCAT", "dummy sequence"
)

With two additional methods, we now have a pipeline to convert dna into rna, and rna into a protein sequence:

dna = biojava.DNAfromPlainSequence("GCATATGAA")
rna = biojava.transcriptionOf(dna)
prot = biojava.translationOf(rna)

The bridgedb manager

BridgeDb is a platform for identifier mapping [3]. The Bioclipse manager makes its functionality available.

At the core, BridgeDb is a framework, but the project also provides actual identifier mapping databases. And, of course, when you want to use id mapping functionality, you first need to load such a database. The plugin is written such that id mapping databases can be downloaded as Bioclipse plugins, and the extension mechanism allows the manager to list which mapping databases are available:

dbList = bridgedb.listIDMapperProviders()

And then the available mapping databases can be loaded, for example, the first in this example:

mbMapper = bridgedb.getIDMapper(dbList.get(0))

Mind you, BridgeDb has separate identifier mapping databases for genes and proteins and for metabolites.

And once we have a mapper then we can start converting identifiers:

casXref = bridgedb.xref("50-00-0", "Ca")
mappings = bridgedb.map(mbMapper, casXref)

References

  1. Holland RCG, Down TA, Pocock M, Prlić A, Huen D, James K, et al. BioJava: an open-source framework for bioinformatics. Bioinformatics. 2008 Sep 15;24(18):2096–7. doi:10.1093/BIOINFORMATICS/BTN397 (Scholia)
  2. Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, et al. BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics. 2012 Oct 15;28(20):2693–5. doi:10.1093/BIOINFORMATICS/BTS494 (Scholia)
  3. van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, et al. The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinf. 2010 Jan 4;11(1):5. doi:10.1186/1471-2105-11-5 (Scholia)