ABSTRACT
Next-generation sequencers are revolutionizing our ability to sequence the genomes of new algae efficiently and in a cost effective manner. Several assembly tools have been developed that take short read data and assemble it into large continuous fragments of DNA. Gene prediction tools are also available which identify coding structures within these fragments. The resulting transcripts can then be analyzed to generate predicted protein sequences. The function of these protein sequences are subsequently determined by searching for close homologs in protein databases and transferring the annotation between the two proteins. While some versions of the previously described data processing pipeline have become commonplace in genome projects, the resulting functional annotation is typically fairly minimal and includes only limited biological pathway information and protein structure annotation. In contrast, the integration of a variety of pathway, function and protein databases allows for the generation of much richer and more valuable annotations for each protein.
