BIOF Files

1)BIOF_Descriptions.xls - restriction enndonucleases table. May be updated by other enzymes, file format should be Excel 2003, *.xlsx file will not be recognized by the program.

The list of available RE, used by BIOF for mapping, is a single Microsoft Excel file, with 3 mandatory fields for each enzyme – cohesive end sequence, recognition site and enzyme name. Blunt-end or non-palindromic RE can be added to the list, then they will be included in the mapping output, but will not be used for generation of hybrid sites.

RE used represent commercially available type II restriction enzymes (REBASE version 112) with non-ambigous, palindromic hexanucleotide recognition site, generating 5’ sticky ends upon cutting.


2) BIOF will create sub-folder BIOF_Fragments for *.txt files, containing DNA fragments under analyses and sub-folder BIOF_Findings, containing mapping results. 

3) DNA sequence for analysis can be pasted from the clipboard (Ctrl+V or «Paste») or loaded as a FASTA-formatted or plain text file. Sequence can be further edited by standard editing keys (Ctrl and Z to undo, X to cut, C to copy, V to paste). 

4) Use «Execute» button to start analysis. 

5) In the «Results» pane - list of RE or hybrid RE sites positions is shown. There are three columns in the «Results» pane – 1) position of the RE site (starting coordinate, not the site of the RE cut), 2) RE recognition string or two strings – for hybrid sites 3)enzyme name or two names – for hybrid sites. 
Nucleotides which will form the cohesive ends after RE cut are shown in CAPITAL letters. 
In the «Enzymes» pane recognition strings of RE’s are listed. 

In the upper sequence pane RE or hybrid RE sites are shown by coloured font (green and red fonts respectively).

If a particular RE is chosen in the «Results» pane – it becomes automatically selected in upper sequence pane. If the cursor in the sequence pane is placed on a particular RE site, after pressing «position» button – corresponding RE becomes automatically selected in the «Results» pane. If the cursor in the sequence pane is placed not inside the RE site, after pressing «position» button – the nearest RE becomes automatically selected in the «Results» pane.