Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M.. KAAS: an automatic genome annotation and pathway reconstruction server. Nucl Ac Res 35: W182-W185

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
Nucleic Acids Research (Impact Factor: 9.11). 08/2007; 35(Web Server issue):W182-5. DOI: 10.1093/nar/gkm321
Source: PubMed


The number of complete and draft genomes is rapidly growing in recent years, and it has become increasingly important to automate
the identification of functional properties and biological roles of genes in these genomes. In the KEGG database, genes in
complete genomes are annotated with the KEGG orthology (KO) identifiers, or the K numbers, based on the best hit information
using Smith–Waterman scores as well as by the manual curation. Each K number represents an ortholog group of genes, and it
is directly linked to an object in the KEGG pathway map or the BRITE functional hierarchy. Here, we have developed a web-based
server called KAAS (KEGG Automatic Annotation Server: i.e. an implementation of a rapid method to automatically assign K numbers to genes in the genome, enabling reconstruction
of KEGG pathways and BRITE hierarchies. The method is based on sequence similarities, bi-directional best hit information
and some heuristics, and has achieved a high degree of accuracy when compared with the manually curated KEGG GENES database.

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    • "Multiple testing correction (False Discovery Rate) was used for differential expression analysis (Benjamini and Hochberg, 1995). Features of the array were annotated using BLAST 2.2.29+ (blastx) against the entire non-redundant protein database as well as using the KEGG Automatic Annotation Server to obtain functional annotations (Altschul et al. 1990 and Moriya et al. 2007). A total of 89.6 % of all probes were returned with a BLAST annotation (annotation date Dec 2014) with e-value < 0.001, while 59 % of probes were returned with a functional annotation (KEGG identifier) using the KAAS server. "
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    Comparative Biochemistry and Physiology Part D Genomics and Proteomics 12/2015; 16:48-58. DOI:10.1016/j.cbd.2015.07.005 · 2.06 Impact Factor
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    • "Gene ontology term enrichment was analysed by the GoPipe program using a BLASTP search against the Swiss-Prot and TrEMBL databases (Chen et al., 2005). KEGG pathway annotations were performed using the KEGG Automatic Annotation Server (KAAS) using the bidirectional best-hit information method (Moriya et al., 2007). "
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    ABSTRACT: As a perennial forage crop broadly distributed in eastern Eurasia, sheepgrass (Leymus chinensis (Trin.) Tzvel) is highly tolerant to low-temperature stress. Previous report indicates that sheepgrass is able to endure as low as -47.5 °C,allowing it to survive through the cold winter season. However, due to the lack of sufficient studies, the underlying mechanism towards the extraordinary low-temperature tolerance is unclear. Although the transcription profiling has provided insight into the transcriptome response to cold stress, more detailed studies are required to dissect the molecular mechanism regarding the excellent abiotic stress tolerance. In this work, we report a novel transcript factor LcFIN1 (L. chinensis freezing-induced 1) from sheepgrass. LcFIN1 showed no homology with other known genes and was rapidly and highly induced by cold stress, suggesting that LcFIN1 participates in the early response to cold stress. Consistently, ectopic expression of LcFIN1 significantly increased cold stress tolerance in the transgenic plants, as indicated by the higher survival rate, fresh weight and other stress-related indexes after a freezing treatment. Transcriptome analysis showed that numerous stress-related genes were differentially expressed in LcFIN1-overexpressing plants, suggesting that LcFIN1 may enhance plant abiotic stress tolerance by transcriptional regulation. Electrophoretic mobility shift assays and CHIP-qPCR showed that LcCBF1 can bind to the CRT/DRE cis-element located in the promoter region of LcFIN1, suggesting that LcFIN1 is directly regulated by LcCBF1. Taken together, our results suggest that LcFIN1 positively regulates plant adaptation response to cold stress and is a promising candidate gene to improve crop cold tolerance. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
    Plant Biotechnology Journal 08/2015; DOI:10.1111/pbi.12435 · 5.75 Impact Factor
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    • "InterPro terms were also obtained from InterProScan at EBI, converted and merged with GOs using Blast2GO software. Finally, the KEGG (Kyoto Encyclopedia of Genes and Genome) orthology (KO) identifiers, or the K numbers, were generated using the web-based server KAAS (KEGG Automatic Annotation Server) (Moriya et al., 2007), resulting in the mapping of putative KEGG metabolic pathways of C. brasiliana. The transcripts assigned to each gene family were first identified based on the closest blastx matches in the NCBI nr database, followed by the identification of at least one of the descriptors provided by the relevant InterPro Scan and Pfam domain (Supplementary Table S2). "
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