The Kiwifruit Information Resource (KIR) is a database and website dedicated to the genomic information of the kiwifruit, which includes eight speices: Actinidia chinensis, Actinidia arguta, Actinidia deliciosa, Actinidia eriantha, Actinidia hemsleyana, Actinidia indochinensis, Actinidia polygama, and Actinidia setosa. This page contains documentation and questions that are useful to the larger KIR user community. Usually, wherever you see a symbol next to a word, click on the symbol to see a definition for the word or phrase. Please let us know if you have a specific topic that you think should be added.

Documentation

Software requirements

The KIR website is designed to work with most common browsers. No additional software is required. We have tested the pages in Firefox 2.0, Safari 2.0 and Microsoft Explorer 7. Conveniently, JavaScript has to be activated for the drop down menus to work properly.

KIR update cycle

The KIR codebase and database are updated weekly, every Friday morning. During the updated, for a short period of time, some links may not work properly. Please notify us if these conditions persist.

Cytoscape web usage

Cytoscape Web is a web-based network visualization tool-modeled. Here, it is integrated into our web pages to visualize and analyze the involving protein interactions and corresponding members, where proteins and interactions are graphed as nodes and edges, respectively. The Adobe Flash plugin is required.

Frequently Asked Questions (FAQs)

Question: What do the identifiers of the format Ach08g150811 and Ach08g150811.2 mean?

Answer: These identifiers denote predicted gene and protein forms from the kiwifruit genome sequencing project. "Ach" is the 3 letter abbreviation of Actinidia chinensis, the 2 digit number following the 'Ach' denotes the chromosome, 'g' denotes that the sequence is a gene, and the 6 digit number following the 'g' identifies the gene on the chromosome, starting at the top and counting in 10 increments. The dot together with any number followed denotes the transcript (a locus can give rise to many transcripts, splice variants, distinguished by different number), and also the proteins derived from these transcripts.

Question: Kiwifruit genome has 29 chromosomes. However, some sequences are mapped to 'chr00'. What is 'chr00'?

Answer: Chr00 is a place holder for kiwifruit sequences that could not be mapped to any of the 29 kiwifruit chromosomes.

Question: How can I download annotation features on the kiwifruit genome?

Answer: As an alternative to Jbrowse's download function, you can use this tool to select your region of interest and download the features using the download options at the top right of the page.

Question: How can I convert gene/protein identifers between different versions of annotation?

Answer: Up to now, we have published two versions of kiwifruit genome annotation. The ID Converter service in TOOLS section allows users to programmatically convert the ID between different versions. Only one protein identier per line is allowed.