PATTERNFINDER

Human c-myc DNA, 5' regulatory region, 2.5 kb:

- Open file containing c-myc sequence: c-myc_seq.txt
- Select All, Copy and Paste into the "DNA SEQUENCE QUERY" window of PATTERNFINDER or the BATCH version.
- Use the browser "BACK" and "FORWARD" functions to navigate between the DEMO files and programs.

In the EXAMPLES below, select "Analyze the Whole Molecule" and query the DNA sequence c-myc_seq.txt :

PATTERNFINDER with THERMOCALC (Fig. 1A):

- Open file AvaI site plus 36 bp 3': AvaI_n36.txt
- Select All, Copy and Paste into "ENTER A PATTERN" window.
- In "Maximum Pattern Span (bp):" window, enter 42
- Select checkbox to enable THERMOCALC and enter:

- Start Position 1

BATCH PATTERNFINDER (Fig. 1B):

- Open Batch file: Batch_myc.txt
- Select All, Copy and Paste into "BATCH OF QUERIES" window. Make sure that the cursor is at the END of the last line.

- If not, delete any "Enter" keys inadvertantly pasted or typed and return the cursor to the END of the last line.

PATTERNFINDER with WEB-THERMODYN (Fig. 1C):

- Open file FBP_3 site plus 200 bp 5' & 3': FBP3_n200.txt
- Select All, Copy and Paste into "ENTER A PATTERN" window.
- In "Maximum Pattern Span (bp):" window, enter 408
- Select checkbox to enable WEB-THERMODYN and enter:

- Start Position 1 | Step Size 1 | Window Size 42 | Number of Markers 1

- Submit Query. On the Result Page, scroll down to the BOTTOM, then click the "W-T it!" button.