Abstract
AbsatractAlong with the constant improvement in high-throughput sequencing technology, an increasing number of transcriptome sequencing projects are carried out in organisms without decoded genome information and even on environmental biological samples. To study the biological functions of novel transcripts, the very first task is to identify their potential functions. We present a web-based annotation tool, FunctionAnnotator, which offers comprehensive annotations, including GO term assignment, enzyme annotation, domain/motif identification and predictions for subcellular localization. To accelerate the annotation process, we have optimized the computation processes and used parallel computing for all annotation steps. Moreover, FunctionAnnotator is designed to be versatile, and it generates a variety of useful outputs for facilitating other analyses. Here, we demonstrate how FunctionAnnotator can be helpful in annotating non-model organisms. We further illustrate that FunctionAnnotator can estimate the taxonomic composition of environmental samples and assist in the identification of novel proteins by combining RNA-Seq data with proteomics technology. In summary, FunctionAnnotator can efficiently annotate transcriptomes and greatly benefits studies focusing on non-model organisms or metatranscriptomes. FunctionAnnotator, a comprehensive annotation web-service tool, is freely available online at: http://fa.cgu.edu.tw/. This new web-based annotator will shed light on field studies involving organisms without a reference genome.
Highlights
With the improvement of sequencing technology, Next-Generation Sequencing (NGS) has been used increasingly frequently for transcriptome studies[1]
We propose a successor to FastAnnotator, FunctionAnnotator, which focuses on providing comprehensive functional annotations and generating more output files that could be valuable in further downstream analyses
Metatranscriptomics can be a surrogate for metagenomics, in terms of its potential for understanding the community composition of environmental samples
Summary
FunctionAnnotator provides comprehensive and efficient annotation for transcriptomes from non-model organisms. With the most updated database and integration of more functional prediction tools (including taxonomic distribution, transmembrane domain, subcellular localization, lipoprotein and signal peptide prediction), FunctionAnnotator provides functional annotation for 35,971 contigs out of 56,263 contigs that have predicted amino acid sequences of more than 66 amino acids. From GO term annotation, we found that the most abundant molecular functions in this clam transcriptome are ion binding, hydrolase activity, nucleotide binding, protein binding, transferase activity and nucleic acid binding (Fig. 2c) These results are consistent with previous studies, which show that the most abundant molecular function for transcripts is “binding” in clam (Meretrix meretrix), whelk (Rapana venosa), Eastern oyster (Crassostrea virginica) and Pacific oyster (Crassostrea gigas)[25,26,27,28]. These 2,299 entries may be incomplete transcripts derived from low coverage
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