algal functional annotation tool a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data藻功能注释工具套件的功能解释网络分析大型基因列表使用集成的注释和表达数据.pdfVIP

Lopez et al. BMC Bioinformatics 2011, 12:282 /1471-2105/12/282 DATABASE Open Access Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data 1 1 1 2,3 1,3* David Lopez , David Casero , Shawn J Cokus , Sabeeha S Merchant and Matteo Pellegrini Abstract Background: Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of ‘interesting’ genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. Description: The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pat