The directory \Databases_S_paradoxus\ contains folders with the following files:

1. Files that contain "Database" in their name (Datebase_genes, Database_IGR): 
   represent Access databases. These databases are designed for calculation of deltaG average,deltaG minimum and it's position of different features (genes, IGRs).
2. Files that contain "Delta" in their name: these are .txt files that contain thermodynamic data 
There are two types of "Delta" files:
-Delta_RD:contain information about ΔG of RNA/DNA duplexes duplexes. RNA is identical to Watson coding strand
-Delta_DR: consists of tab delimited .txt files that contain information about ΔG of RNA/DNA duplexes.RNA is identical to Crick coding strand
3. "spar_contigs_N": contains the concatenate sequence of all S.paradoxus contigues separated by 100"N" added at the start of each contigue in order to avoid artificial windows
 between different contigues.This file can be used as an input file in the Perl software. 
4. "Spar_original&new_coord.xls": contains the original ORF coordinates and the new ones in the concatenate sequence

The Access databases: Datebase_genes, Database_IGR contain:

1.Tables:

 1.1. Delta: an empty table in which the  .txt file containing thermodynamic data (see above) should be imported.This table is used by the 
module "Transform" to generate table "DeltaG"
The table contains two columns, named:
 
      -position_bp: the medium position number of a given window 
      -DeltaG: the free energy delta G of each window

 1.2. Genes:in spite of its name this table is filled with information about a given feature (genes, IGRs). This table is used by the 
module "Transform" to generate table "DeltaG"

The table contains two columns, named:
      -chr: chromosome number
      -ORF:features' names
      -position_start:coordinates of features' starts
      -position_end:coordinates of features' ends

Note: In Database_IGR there are three tables containing "Genes" in their name: 
"Genes" :an empty table , presented in the database in order to preserve the structures of the queries; 
"Genes_W": contains information about the coordinates of the IGRs 3' to Watson's ORFs; 
"Genes_C": contains information about the coordinates of the IGRs 3' to Crick's ORFs; 
To calculate delta G of one of these features (3' to Watson's or 3'to Crick's ORFs) you should delete "Genes" and rename "Genes_w" or "Genes_C" to 
"Genes"

 1.3. DeltaG: an empty accessory table that should be filled by running the Module "Transform". Then the 
      table would be filled with the following data: the name of each feature in column "ORF" and the position of each nucleotide within the borders of the 
      feature in column "position_bp".

Note: All the tables should be filled with data before running the Queries

2.Queries:
 
 2.1.  Avg: generates a table containing the columns:
      - ORF:features' names
      - AvgOfDeltaG: the average values of delta G for a given feature
 2.2.  Result: generates a table containing the columns:
      -ORF: features' names
      -All.DeltG: delta G minimum in a given feature
      -FirstOfposition_bp: the exact positions of delta G minimums 

 2.3. 0_RunMeOnly:an accessory query, necessary for runnin query "Result"
 2.4. All: an accessory query, necessary for runnin query "Result"
 2.5. All_min: an accessory query, necessary for runnin query "Result"
 
Note: Using "Delta_RD" files (see above) you will calculate ΔG of sense mRNA/DNA duplexes of Watson’s ORFs and their corresponding features and 
ΔG of antisense RNA/DNA duplexes of Crick’s ORFs and their corresponding features. 
Using "Delta_DR" files (see above) you will calculate ΔG of sense mRNA/DNA duplexes of Crick’s ORFs and their corresponding features and 
ΔG of antisense RNA/DNA duplexes of Watson’s ORFs and their corresponding features. 

3. Modules:
 3.1 Transform: generates the accessory table DeltaG by double click on "Transform" and then in the menu bar click Run,
     and then click Run.