bio.i.md

Bioinformatics

The biojava manager

BioJava is a library oriented at dna, rna, and protein sequences [Q24654080,Q24630147]. 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:

DNAfromPlainSequence

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 [Q28842753]. 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