Recent development in the high-throughput sequencing (HTS) technology makes it feasible to sequence the complete transcriptome from a non-model organism or even metatranscriptome from environmental samples. The next challenge after generating hundreds of millions of sequences is to annotate these transcripts and classify the transcripts based on their putative functions. Since most of the biological scientists do not have knowledge to install Linux based software packages or to maintain different databases used for transcript annotation, we developed an automatic annotation tool with easy-to-use interface.

In order to elucidate the potential functions of transcripts, we integrated the well-established annotation tools: Blast2GO, PRIAM and RPS BLAST in a web-based service named FastAnnotator which can assign GO terms, EC numbers and functional domains to query sequences.

The annotation in FastAnnotator includes four main parts, finding best hits in NCBI nr database, assigning GO terms, identifying enzymes, and identifying domains. As the assignment of GO terms actually needs to utilize the result from LAST searching against NCBI nr database, these four main steps can be divided into three independent modules: GO terms assignment, enzyme identification, domain identification as shown in following figure. FastAnnotator runs these three steps in parallel to speed up the annotation procedure. FastAnnotator also calculates basic statistics of input sequences and provide a statistical report in the result.

FastAnnotator was published in 2012 BMC Genomics supplements.
Please cite "Chen TW, Gan RCR, Wu TH, Huang PJ, Lee CY, Chen YYM, Chen CC and Tang P*. (2012) FastAnnotator: an efficient transcript annotation web tool. BMC Genomics 13:Suppl 7, S9" if you used FastAnnotator for your publication