files IsoFinder_DOS.zip (Windows) or IsoFinder_Linux.zip (Linux Debian)
on a local directory, then obtaining the executable file 'isofinder'.
On a command-line
window (DOS), change to the working directory containing the data and
isofinder <DNA file> <Sig.Level> <Sig.Method> <Win.Size>
terminal and type:
DNA File: File contaning the DNA sequence (EMBL,GenBank and FASTA
formats are allowed)
level: Statistical significance required to accept a new cut (e.g.
0.99 will accept less cuts than 0.95)
size for coarse graining: Window size to filter out short-scale
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 for details):
p1 Parametric (t-student)
p2 Parametric (t-student) with different variances
p3 Parametric for maximum value
file: File to write the LHGR list in ASCII.
segmentation is finished the program generates the following files:
iso_DNAfile.coo: List with LHGR's coordinates (ASCII)
List with LHGR's coordinates