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