;
; THE BEST WAY to read this file is to use plain text editor,
; which does not wrap contents of isolated lines along several
; lines on screen. For example, with Microsoft(R) Windows(TM)
; operating systems use program "Notepad" and disable menu option
; "Format/Word Wrap".
;
; ==================================================================
;
; This is an exemplar parameter file for the program:
;
; *****  BEsTRF: Best Estimated Terminal Restriction Fragment  *****
;
; Purpose of the program:
;
; BEsTRF provides an in-depth and controlled environment for up 
; to date exploration of Primers-Enzymes-Gene sections combinations 
; used in T-RFLP.
; User defined sequence database can be processed and the resolution
; of user specified sets of Primers and restriction endonucleases
; can be analyzed on either forward or reverse terminal fragments.
; 
; Suggested citation: 
;
; B. Stres, J.M. Tiedje, B. Murovec, BEsTRF: a tool for optimal
;    resolution of terminal restriction fragment length polymorphism
;    analysis based on user defined primer-enzyme-sequence databases,
;    Submitted for publication in journal Bioinformatics
;
; Please check our web site 
;
;              http://lie.fe.uni-lj.si/bestrf
;
; for reference updates.
;
;
;
; ==================================================================
;
; DISCLAIMER: this program is developed with the best effort to make
;             it error-free and working as described.
;             However, there are no guarantees.
;
;             The developers do not take any responsibilities
;             whatsoever if the use or misuse of the program causes
;             or leads to personal injuries, data loss, material
;             damage or any other undesired consequences.
;
;             Under no conditions should the developers be charged 
;             or prosecuted by anyone using the program for any
;             reason whatsoever.
; 
; ==================================================================
;





;*******************************************************************
;
; I. Input FASTA sequences
;
;*******************************************************************



;DNA_File_Names "my_new_seqs.txt"

;Max_DNA_Degeneration	4 ; set the value to 4, 3, 2 or 1 (or 0)





;*******************************************************************
;
; II. Primers discovery specification
;
;*******************************************************************



;Forward_Primer_Dictionary        F_my_new_primers.txt
;Reverse_Primer_Dictionary        R_my_new_primers.txt

;Forward_Primers "968f 341f"
;Reverse_Primers "1406r"

;Max_Primer_Degeneration  4 

;Strict_Primer_Match   No

;Primer_Matches_Aligned_Sites_Only   no

;Primer_Mismatches     0

;Primer_Levenshtein  no
;Primer_Insertion_Cost      2
;Primer_Deletion_Cost       2
;Primer_Wrong_Code_Cost     1
              
;Primer_Look_Ahead  2

;Max_Degeneration_Between_Primers 4

;Revert_DNA_When_No_Match   no





;*******************************************************************
;
; III. Enzymes discovery specification
;
;*******************************************************************



;Enzyme_Dictionary	"Dict1.txt Dict2.txt Dict3.txt"

;Enzymes   "AbsI CC^GG AbaI GCTA"

;Max_Enzyme_Degeneration            4

;Strict_Enzyme_Match                no

;Enzyme_Matches_Aligned_Sites_Only  no

;Enzyme_Mismatches                  0

;Enzyme_Look_Ahead                  4

;Max_Fragment_Degeneration    8

;Treat_No_Enzyme_As_Full_Hit   yes ; set the value to Yes or No





;*******************************************************************
;
; IV. Output specification
;
;*******************************************************************



;Output_Directory_Root          genetic_engineering
;Output_Directory_Append_Date   yes

;Primer_Output_File_Name "primer_results.txt"
;Forward_Output_File_Name 	"enzyme_forward_results1.txt"
;Forward_Alt_Output_File_Name	"enzyme_forward_results2.txt"
;Reverse_Output_File_Name 	"enzyme_reverse_results1.txt"
;Reverse_Alt_Output_File_Name 	"enzyme_reverse_results2.txt"
;Forward_Enzyme_Fragments_File_Name "fwd_fragments.txt"
;Reverse_Enzyme_Fragments_File_Name "rev_fragments.txt"

;Table_Header   yes ; set the value to Yes or No

;Number_of_Best_Primer_Histograms   7
;Minimal_Primer_Histogram_Entries   all
;Number_of_Best_Results      12
;Number_of_Best_Histograms   all
;Minimal_Histogram_Entries   3

;Rejected_No_Primers     rejected_NP.txt
;Rejected_No_Enzymes     rejected_NE.txt

;Accepted_File_Name    accepted.txt

;Accepted_Requires_Enzyme_Match false

;Group_Accepted_Into_Files    true

;Drop_Blanks_From_Rejected   no ; set the value to Yes or No
;Drop_Blanks_From_Accepted   no ; set the value to Yes or No

;Use_Locale_Settings yes

;TRF_Phylogeny_Report     yes ; set the value to Yes or No
;Drop_Blanks_From_TRF_Phylogeny_Report   no ; set the value to Yes or No