著者

Yuuichi Nakano Mitsuo Iwadate Hideaki Umeyama Y-h. Taguchi

出版者

一般社団法人 情報処理学会

雑誌

IPSJ Transactions on Bioinformatics (ISSN:18826679)

巻号頁・発行日

vol.7, pp.2-15, 2014 (Released:2014-01-17)

参考文献数

15

被引用文献数

1

---

Type III secretion system (T3SS) effector protein is a part of bacterial secretion systems. T3SS exists in the pathogenic and symbiotic bacteria. How the T3SS effector proteins in these two classes differ from each other should be interesting. In this paper, we successfully discriminated T3SS effector proteins between plant pathogenic, animal pathogenic and plant symbiotic bacteria based on feature vectors inferred computationally by Yahara et al. only from amino acid sequences. This suggests that these three classes of bacteria employ distinct T3SS effector proteins. We also hypothesized that the feature vector proposed by Yahara et al. represents protein structure, possibly protein folds defined in Structural Classification of Proteins (SCOP) database.

著者

Yuuichi Nakano Mitsuo Iwadate Hideaki Umeyama Y-h. Taguchi

出版者

Information and Media Technologies 編集運営会議

雑誌

Information and Media Technologies (ISSN:18810896)

巻号頁・発行日

vol.9, no.1, pp.141-154, 2014 (Released:2014-03-15)

参考文献数

15

---

Type III secretion system (T3SS) effector protein is a part of bacterial secretion systems. T3SS exists in the pathogenic and symbiotic bacteria. How the T3SS effector proteins in these two classes differ from each other should be interesting. In this paper, we successfully discriminated T3SS effector proteins between plant pathogenic, animal pathogenic and plant symbiotic bacteria based on feature vectors inferred computationally by Yahara et al. only from amino acid sequences. This suggests that these three classes of bacteria employ distinct T3SS effector proteins. We also hypothesized that the feature vector proposed by Yahara et al. represents protein structure, possibly protein folds defined in Structural Classification of Proteins (SCOP) database.

著者

Daichi Nogami Yuuichi Nakano Y-H.Taguchi

雑誌

研究報告バイオ情報学(BIO)

巻号頁・発行日

vol.2013-BIO-34, no.28, pp.1-2, 2013-06-20

---

Inference of subcellular location only using sequence information is important. In this paper, we proposed the application of principal component analysis-based linear discriminant analysis for subcellular location information. It achieved the performance of Area Under the Curve under Receiver Operating Characteristic curve mostly more than 0.95 if less than 80% sequence identity non-redundancy was applied.

著者

Yuuichi Nakano Mitsuo Iwadate Hideaki Umeyama Y-H.Taguchi

雑誌

研究報告バイオ情報学(BIO)

巻号頁・発行日

vol.2013-BIO-34, no.10, pp.1-8, 2013-06-20

---

Type III secretion system (T3SS) effector protein is a part of bacterial secretion systems. T3SS exists in the pathogenic and symbiotic bacteria. How the T3SS effector proteins in these two classes differ from each other should be interesting. In this paper, we proposed the usage of principal component analysis based linear discriminant analysis that discriminates T3SS effector proteins between plant pathogenic, animal pathogenic and plant symbiotic bacteria by the accuracy of 0.77. We also hypothesized that the feature vector proposed by Yahara et al represents protein structure, possibly protein folds defined in Structural Classification of Proteins (SCOP) database.