Welcome to FR Database 1.0


Key words : fruit, development, ripening

USAGE: 

1.  Search You can input keywords to search the FR database. The search fields include FR ID, Gene/Protein Names, Uniprot ID, Species, Development Stage, and Localization.

Example: Please click on the Species field in the combo box to search "Solanum lycopersicum". By clicking on the "Submit" button, the 265 related fruit development and ripening genes/proteins will be shown.


2.  Advanced search Advanced search allows you to input up to three terms to find the information more specifically. The querying fields can be empty if fewer terms were needed. The three terms could be connected by the following operators:

and: the term following this operator has to be included in the specified field(s).

or: either the preceding or the following term to this operator should occur in the specified field(s).

exclude: If selected, the term following this operator must be not contained in the specified field(s).

Example: You can click on the "Example" button to load an instance, which could search "IF (Immature Fruit)" and "SR (Stress Resistance)" in tomato. And 15 genes/proteins involved in stress resistance during tomato immature period will be shown by clicking on the "Submit" button.


3.  Orthology Search You can input a specified FR id that is included in FR database. The Identity, E-value and BLAST Score thresholds could be user-defined.

Example: You can click on the "Example" button to browse the FR01Sl00631 (DNA damage-binding protein 1) orthologous in Arabodopsis.



FAQs: 

1.  What do the identifiers of the format FR01Sl00631 mean ?

Answer: These identifiers denote genes and proteins form. "FR01" denotes the first version of FR database. The 2 letters following the "FR01" is the abbreviation of species where this gene/protein is from (use this file  ), and the last 5 digit number identifies the gene/protein with counting in a single increment.


2.  What platforms does the Jmol application run on ?

Answer: Jmol is a java applet that works in web browsers. In order to run and use it needs your system to have a suitable Java Runtime Environment (JRE) installed. Before you try to run Jmol you should therefore ensure that you have a suitable JRE. You could get JREs for different platforms available from "www.java.com". And you are strongly advised to install 64-bit Java if your system is 64-bit. Additionally, there are two tips: first, the Java safety setting should be tune to "medium"; second, when security prompt asks for confirmation before allowing Java content to run in the browser, we should always "activate" to enable.


3.  Where are the protein structure visualized in Jmol from ?

Answer: The PDB structures for my analysis are obtained from PDB database if the protein structures have been solved by the experimental methods. Otherwise the PDB structures are built through homology modeling via the fully automated server, SWISS-MODEL.


4.  What does the color in the "development stage" topic mean ?

Answer: The five different color signifies the five sequential development period of fruit: the blue color signifies immature fruit (IF), the green color signifies mature green (MG), the pink color signifies breaker (BR), the red color signifies ripe fruit (RF), and the purple color signifies post harvest (PH).


5.  What does the letter "s" in parentheses following some gene names stand for ?

Answer: If the letter "s" is labelled after corresponding gene name, it means that gene is expressed specifically in fruit, e.g. FR01Vv00354.