Browsing by Author "Gan, Ruei-Chi Richie"

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FastAnnotator- an efficient transcript annotation web tool
(2012-12-13)
Chen, Ting-Wen
;
Gan, Ruei-Chi Richie
;
Wu, Timothy H.
;
Huang, Po-Jung
;
Lee, Cheng-Yang
Background: Recent developments in high-throughput sequencing (HTS) technologies have made it feasible to sequence the complete transcriptomes of non-model organisms or metatranscriptomes from environmental samples. The challenge after generating hundreds of millions of sequences is to annotate these transcripts and classify the transcripts based on their putative functions. Because many biological scientists lack the knowledge to install Linux-based software packages or maintain databases used for transcript annotation, we developed an automatic annotation tool with an easy-to-use interface. Methods: To elucidate the potential functions of gene transcripts, we integrated well-established annotation tools: Blast2GO, PRIAM and RPS BLAST in a web-based service, FastAnnotator, which can assign Gene Ontology (GO) terms, Enzyme Commission numbers (EC numbers) and functional domains to query sequences. Results: Using six transcriptome sequence datasets as examples, we demonstrated the ability of FastAnnotator to assign functional annotations. FastAnnotator annotated 88.1% and 81.3% of the transcripts from the well-studied organisms Caenorhabditis elegans and Streptococcus parasanguinis, respectively. Furthermore, FastAnnotator annotated 62.9%, 20.4%, 53.1% and 42.0% of the sequences from the transcriptomes of sweet potato, clam, amoeba, and Trichomonas vaginalis, respectively, which lack reference genomes. We demonstrated that FastAnnotator can complete the annotation process in a reasonable amount of time and is suitable for the annotation of transcriptomes from model organisms or organisms for which annotated reference genomes are not avaiable. Conclusions: The sequencing process no longer represents the bottleneck in the study of genomics, and automatic annotation tools have become invaluable as the annotation procedure has become the limiting step. We present FastAnnotator, which was an automated annotation web tool designed to efficiently annotate sequences with their gene functions, enzyme functions or domains. FastAnnotator is useful in transcriptome studies and especially for those focusing on non-model organisms or metatranscriptomes. FastAnnotator does not require local installation and is freely available at http://fastannotator.cgu.edu.tw.
Phosphoproteome profiling of the sexually transmitted pathogen Trichomonas vaginalis
(2013-10-01)
Yeh, Yuan-Ming
;
Huang, Kuo-Yang
;
Gan, Ruei-Chi Richie
;
Huang, Hsien-Da
;
Wang, Tzu-Chien V.
Background/Purpose(s): Trichomoniasis caused by Trichomonas vaginalis is the most common non-viral sexually transmitted infection. Morphological transformation from the trophozoite stage to the amoeboid or pseudocyst stage is crucial for T. vaginalis infection and survival. Protein phosphorylation is a key post-translational modification involved in the regulation of several biological processes in various prokaryotes and eukaryotes. More than 880 protein kinases have been identified in the T. vaginalis genome. However, little is known about the phosphorylation of specific proteins and the distribution of phosphorylated proteins in different stages of the morphological transformation of T. vaginalis. Methods: To obtain a more comprehensive understanding of the T. vaginalis phosphoproteome, we analyzed phosphorylated proteins in the three morphological stages using titanium dioxide combined with LC-MS/MS. Results: A total of 93 phosphopeptides originating from 82 unique proteins were identified. Among these proteins, 21 were detected in all stages, 29 were identified in two different stages, and 32 were stage specific. Conclusion: Identification of stage-specific phosphorylated proteins indicates that phosphorylation of these proteins may play a key role in the morphological transformation of T. vaginalis. Copyright (C) 2012, Taiwan Society of Microbiology. Published by Elsevier Taiwan LLC. All rights reserved.