KOBAS server: a web-based platform for automated annotation and pathway identification

There is an increasing need to automatically annotate a set of genes or proteins (from genome sequencing, DNA microarray analysis or protein 2D gel experiments) using controlled vocabularies and identify the pathways involved, especially the statistically enriched pathways. We have previously demonstrated the KEGG Orthology (KO) as an effective alternative controlled vocabulary and developed a standalone KO-Based Annotation System (KOBAS). Here we report a KOBAS server with a friendly webbased user interface and enhanced functionalities. The server can support input by nucleotide or amino acid sequences or by sequence identifiers in populardatabasesandcanannotatethe input withKO terms and KEGG pathways by BLAST sequence similarity or directly ID mapping to genes with known annotations. The server can then identify both frequent and statistically enriched pathways, offering the choices of four statistical tests and the option of multiple testing correction. The server also has a `User ...

• Type: Journal
• Year: 2006
• Where: NAR
• Authors: Jianmin Wu, Xizeng Mao, Tao Cai, Jingchu Luo, Liping Wei
• Keywords: Alternative Controlled Vocabulary, DNA Microarray Analysis, KOBAS Server, NAR 2006