RRE is a tool to extract non-coding regions associated to annotated genes.

RRE tools: 

• RRE is a sequence parser written in JAVA. RRE parser uses the gene/mRNA/CDS features in GBS/GBK files to extract the annotated regions from the corresponding FA file. RRE saves the extracted regions in various formats (e.i. fasta,xml) and it can populate automatically a MySQL database (www.mysql.com).
  In order to run it RRE and Java 1.4 (java.sun.com/j2se/) has to be installed in the system. 
  
• In order to keep updated the non-coding information an automatic download robot based on CURL was integrated with RRE (the download robot has been implemented only for  PCs running Linux). The tool allows to download new genomic data releases (GBS/GBK and FA/MFA files) when they are available at NCBI.  Download:  rre.tgz (Windows/unix), sample data and windows/unix script file to run RRE parser data.tgz .
  To run rre it is necessary to download from NCBI *.gbs and *.fa or *.gbk files related to the organism of interest.
  
• RRE help menu
• Usage
• Installation

• Rules used in rre for the extraction of regulative regions from gbs/gbk files: If .gbs and .fa files are available .gbs annotations are used to extract sequence data from .fa file. If .gbk files are the only available rre extract a .fa file from the data present in .gbk. 5'UTRs are extracted starting from the mRNA and CDS annotation using the following rule: given the following gbs annotations mRNA = (m1..m2,m3..m4,m5..m6,m7..m8,...,Mx..My) and CDS = (C1..C2,.........,Cx..Cy) where CDS is included in mRNA, 5UTR starts at m1, contains the joining of all the exons upstream CDS an ends at C1 3'UTRs are extracted starting from the mRNA and CDS annotation using the following rule: given the following gbs annotations mRNA = (m1..m2,m3..m4,m5..m6,m7..m8,...,Mx..My) and CDS = (C1..C2,.........,Cx..Cy) where CDS is included in mRNA, 3'UTR  starts at Cy contains all exons in mRNA and ends at My. Upstream regions are extracted using the following rule: mRNA = (m1..m2,m3..m4,m5..m6,m7..m8,...,Mx..My), Upstream region = N bp upstream m1. Downstream regions are extracted using the following rule: mRNA = (m1..m2,m3..m4,m5..m6,m7..m8,...,Mx..My), Downstream region = N bp upstream My. Exons related to CDS are extracted using the following rule: mRNA = (m1..m2,m3..m4,m5..m6,m7..m8,...,Mx..My), CDS = (C1..C2,.........,Cx..Cy), Exon = Range Mi..Mj where Mi>C1, Mj<Cy belonging to mRNA sequence Exons related to the non coding part of mRNA (upstream) are extracted using the following rule: mRNA = (m1..m2,m3..m4,m5..m6,m7..m8,...,Mx..My), CDS = (C1..C2,.........,Cx..Cy), Exon = Range Mi..Mj where Mi>m1, Mj<C1 belonging to mRNA sequence Exons related to the non coding part of mRNA (downstream) are extracted using the following rule: mRNA = (m1..m2,m3..m4,m5..m6,m7..m8,...,Mx..My), CDS = (C1..C2,.........,Cx..Cy), Exon = Range Mi..Mj where Mi>Cy, Mj<My belonging to mRNA sequence Introns related to CDS are extracted using the following rule: mRNA = (m1..m2,m3..m4,m5..m6,m7..m8,...,Mx..My), CDS = (C1..C2,.........,Cx..Cy), Intron = Range Mi..Mj where Mi>C1, Mj<Cy not belonging to mRNA sequence. Introns related to  the non coding part of mRNA (upstream) are extracted using the following rule: mRNA = (m1..m2,m3..m4,m5..m6,m7..m8,...,Mx..My), CDS = (C1..C2,.........,Cx..Cy), Intron = Range Mi..Mj where Mi>m2, Mj<C1 not belonging to mRNA sequence. Introns related to  the non coding part of mRNA (downstream) are extracted using the following rule: mRNA = (m1..m2,m3..m4,m5..m6,m7..m8,...,Mx..My), CDS = (C1..C2,.........,Cx..Cy), Intron = Range Mi..Mj where Mi>Cy, Mj<My not belonging to mRNA sequence. Overlaps between up/downstream regions with gene annotation are handled in the following way: Size definition rule Gene > Upstream > Downstream; example: Gene_b (0..500), mRNA_b (1..400), Gene_a (10000..80000), mRNA_a (40000..50000,60000..70000), Upstream,Downstream size=10000 -> Up Gene_b not extracted, Down Gene_b (401..9999), Up Gene_a (30000..39999), Down Gene_a (70001..80000

• A web based interface to RRE database populated using RRE parser is available here.
• Information about the quieries available at RRE db.