The directory \Databases_S_cerevisiae\Database_DNA_DNA_duplex contains folders with the following files:

1. Files that contain "Database" in their name (Datebase_genes, Database_IGR, Database_EPR, Database_UTR, Database_introns, Database_exons): 
   represent Access databases.These databases are designed for calculation of deltaG average,deltaG minimum and it's position of different features (genes, IGRs, etc.).
2. Files that contain "Delta" in their name: these are .txt files (an output of the Perl software) that contain thermodynamic data at given conditions (window size:win2,9,100 and salt 
   concentration: 10mM, 100mM, 1M)



The Access databases: Datebase_genes, Database_IGR, Database_UTR, Database_introns,Database_exons 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, introns,exons, UTRs). This table is used by the 
module "Transform" to generate table "DeltaG"

The table contains the columns, named:
      
      -ORF:features' names
      -position_start:coordinates of features' starts
      -position_end:coordinates of features' ends

"Database_introns" and "Database_exons" contain additional column named "ID" which contains the ID number in SGD of introns and exons

Note: In Database_IGR and Database_UTR 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 iformation about the coordinates of the IGRs and UTRs 3' to Watson's ORFs; 
"Genes_C": contains iformation about the coordinates of the IGRs and UTRs 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"
 

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.



The Access database "Database_EPR" was designed to measure deltaG of 100bp windows containing the end processing regions (EPRs), positioned in the range
 of 80nt upstream and 20nt downstream from the end of the 3’UTR. Therefore the nucleotide pair indicating position 51bp in the window containing EPR is situated
 30bp upstream of the end of the 3'UTR.
 


"Database_EPR" has different structure. It contains:

1.Tables:
 1.1.EPR:contains the following columns:
     - ORF: name of the transcript's ORF that contain annotated 3'UTR
     - W/C: indicates ORF strand( -1 refers to Crick's ORFs, 1 refers to Watson's ORFs)
     - 3'UTR_length: length(bp) of the 3'UTR
     - 3'UTR_start:coordinates of 3'UTR start
     - 3'UTR_end:coordinates of 3'UTR end
     - EPR: coordinates of the nucleotide pair indicating position 51bp in the EPR's window. 

 1.2. all_chr_DD:an empty table in which the  Delta_DD_10mM_win100.txt file should be imported
 

2. Query:
 
 2.1.EPR_DD:generates a table containing the columns:
      - ORF:name of the transcript's ORF that contain annotated 3'UTR
      - W/C: indicates ORF strand( -1 refers to Crick's ORFs, 1 refers to Watson's ORFs)
      - DeltaG: the values of delta G for a given EPR window