IsoFinderWin
Beta version 

SEGMENTATION OF A SEQUENCE:

Click at the menubar Tools|Segment into LHGRs
It appears a dialog box asking for all the parameters needed for the segmentation:
  • DNA File: File contaning the DNA sequence (EMBL,GenBank and FASTA formats are allowed). You can find the file using the browse button and preview it using ViewFile button.
  • Read sequence from/to: instead of reading the full sequence reads only a subsequence. To read the full sequence write from=1 and to=0 (default)
  • Window lenght for coarse graining: Window size to filter out short-scale heterogeneities.
  • Significance level: Statistical significance required to accept a new cut (e.g. 0.99 will accept less cuts than 0.95)
  • Method to compute the significance: Several methods to estimate the significance of a new cut (see: Oliver et al., Nucleic Acids Research 32, W287-W292 (2004).)
  • Output file: File to write the LHGR list in ascii. You can find the file using the browse button and preview it using ViewFile button.
  • Include GC plot data: By selecting this option the program also writes in the output file the data to make the GC plot of the sequence.
    WARNING: if the sequence is long and window length is small, the output file could
    be very big.

When the segmentation is finished the program shows two windows:
  1. List with LHGR's coordinates
  2. Graphic window with the LHGR map superimposed on top of the GC profile (computed using the window length selected previously)

By default the graph shows the full sequence, to magnify a region move the mouse into the graph, press left button and keeping the button down move the mouse. A box appears showing the region to be magnified. Once the box cover the desired region, release the button and the region will be maximized to cover the full graph. This procedure can be repeated up to 8 times. To recover the graph previous to the magnification press the right button.


VIEW THE GC PROFILE OF A SEQUENCE:

Click at the menubar Files|Show DNA file

It appears a dialog box asking for all the parameters needed for the plot:
  • DNA File: File contaning the DNA sequence (EMBL,GenBank and FASTA formats are allowed). You can find the file using the browse button and preview it using ViewFile button.
  • Read sequence from/to: instead of reading the full sequence reads only a subsequence. To read the full sequence write from=1 and to=0 (default)
  • Window lenght for coarse graining: Window size to filter out short-scale heterogeneities.

The GC plot is showed in a graphical window similar to the one described above.

LOAD A SEGMENTATION PREVIOUSLY COMPUTED:

Click at the menubar Files|Open LHGR file
  • The program shows the list of LHGR coordinates and, if the segmentation was saved with the option "Include GC plot data" selected, also shows the graph with LHGR's superimposed on top of the GC profile.