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Functional Annotation and Database Construction of Amphioxus Hypothetical Proteins

Author: ZhangJian
Tutor: ChenLingLing
School: Shandong University of Technology
Course: Biophysical
Keywords: Amphioxus Protein structure prediction Protein function prediction Protein complex Structure alignment
CLC: Q51
Type: Master's thesis
Year: 2011
Downloads: 78
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Abstract


Amphioxus is a kind of living invertebrate which is most relative to the vertebrates, and it is the "living fossil" used in the study of animal evolution and embryonic development. A large number of amphioxus genes are studied in the laboratories around the world. In 2008, the accomplishment of amphioxus genome sequencing in Florida laid a solid foundation for the future research of amphioxus. More and more evidences for the origin and evolution of vertebrates were provided because of the growing research information of amphioxus molecular biology. However, the functions of some considerable parts of genes are still unknown. Based on the current situation, the structure and function of "hypothetical protein" of amphioxus were predicted and a protein database was constructed (AmphioxusAnnoBase).The characteristics of AmphioxusAnnoBase database were as follows:(ⅰ) 4176 tertiary structures of "hypothetical protein" were predicted by using a series of localized TASSER algorithm, (ⅱ) The potential function of "hypothetical protein" were predicted by FINDSITE algorithm which based on predicted tertiary structures (or known structures), totally 2797 "hypothetical protein" with Gene Ontology were annotated and the ligand binding sites and ligand of 3438 "hypothetical protein" were predicted. The enzyme functions of all "hypothetical protein" were also predicted by EFICAz2 algorithm which based on the protein sequence, the result suggested that there were 206 "hypothetical protein" that may be enzymes, (ⅲ) A prediction of amphioxus protein complex on the whole proteome of the amphioxus was also carried out through comparing yeast and some other model organisms, (ⅳ) Protein complex and the contigs of genome were used and displayed by Cytoscape Web and Gbrowse respectively, (ⅴ) AmphioxusAnnoBase database have been built based on all the above result data by using Apache、PHP、MySQL under the Linux operation system. The result shows as follows:52077 protein sequences were collected from Branchiostoma floridae in Ensemble and Branchiostoma belcheri tsingtauense, Branchiostoma belcheri and Branchiostoma japonicum in NCBI, which can be used freely.In short, AmphioxusAnnoBase can provide more detailed protein function annotation with high accuracy, also it is very easy for the researchers to browse, so it will be meaningful in guiding the following experiments about amphioxus and deeply studying amphioxus functional genes with important theoretical and practical value. AmphioxusAnnoBase Database Web site:http://211.69.128.145/amphioxus/index.php

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CLC: > Biological Sciences > Biochemistry > Protein
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