_{I+1} ^{I} | A | C | G | T |
A | 7.6 | 10.9 | 8.8 | 12.5 |
C | 14.6 | 7.2 | 11.1 | 8.8 |
G | 8.2 | 8.9 | 7.2 | 10.9 |
T | 25 | 8.2 | 14.6 | 7.6 |
Input file format |
a) one line format - only the sequence, without
a header, numbers or spaces, in one line. b) GCG format - if the sequence is given as a file, the sequence itself should start with two dots (..). If the user wishes to add a header- it should precede the two dots. If the sequence is pasted - no header is allowed. Spaces and numbers between bases can be added. c) FASTA format - if the sequence is given as a file, the first line should start with "greater than" sign (>). This line is for the header of the sequence. All the lines that follow should contain the sequence itself. If the sequence is pasted - no header is allowed. Spaces and numbers are between bases can be added. For more details please read the Sequence format page. |
Window size | The number of bases in each window. The window size should be ≥ 2, because the flexibility is calculated for di-nucleotide steps. Default window value - 100 bp |
Leap | The number of bases the window is moved in each step. The leap should be a positive integer. Default leap value - 1 bp |
Threshold Value | The Threshold Value of the twist angle. If the value of the
average twist angle of a window is greater than the Threshold Value-
this window will be defined as a flexible window. The Threshold Value can be zero (and then the whole sequence will be defined as flexible) or any positive number. Default Threshold Value - 13.7 |
Normalization Value |
This variable enables the user to create a common denominator for comparison
of flexibility of sequences with different lengths. The Normalization Value should be a positive integer. Default Normalization Value - 10,000 bp |
Discrete Display Value |
The sequence can be divided into segments. The length of each segment
is the Discrete Display Value. The length of each flexibility peak, the number
of peaks and the number of clusters are added and displayed, for each segment.
This enables the user to easily create a graphic representation of
the results, in which the X-axis is the sequence itself and the units are the
discrete display values. The Y-axis is the total length of the flexibility peaks
or the number of peaks or the number of clusters in each segment. The Discrete Display Value should be a positive integer. Default Discrete Display Value - 100,000 bp |
Minimal number of peaks in a cluster |
The minimal number of peaks that defined a cluster. This minimal number should be a positive integer. Default minimal value - 3 peaks |
Maximal distance between peaks in a cluster |
The maximal number of windows between two adjacent peaks in a cluster.
If the distance between two adjacent peaks is larger than the given maximal distance-
those peaks can not define a cluster. The maximal distance should be a positive integer. Default maximal value - 5,000 windows |
- Output file with the suffix .miscel.out. This file contains: |
a) Parameters of the specific analysis.
b) Total length of the sequence. c) Nucleotides and di-nucleotides composition of the sequence. d) Total length of the peaks and normalized length of the peaks. e) Total length of the unified peaks and normalized length of the unified peaks. f) Average and standard deviation of all the twist angles along the sequence. |
- Output file with the suffix .peaks.out. This file contains: |
a) Parameters of the specific analysis.
b) Total number of peaks. c) Discrete display of the number and length of peaks. d) Peaks ordered by their location in the sequence. For each peak - its location in the sequence, its length, area and nucleotide and di-nucleotide composition. e) Peaks ordered by their length. For each peak - its location in the sequence, its length and area. f) Number of flexibility peaks ordered in groups by their length. g) Total nucleotides and di-nucleotides composition of the peaks. h) Total length of the peaks. i) Average and standard deviation of the lengths of peaks. j) Total number of unified peaks. k) Discrete display of the number and length of unified peaks. l) Unified peaks ordered by their location in the sequence. For each peak - its location in the sequence, its length and nucleotides and di-nucleotides composition. m) Unified peaks ordered by their length. For each peak - its location in the sequence and its length. n) Number of unified peaks ordered in groups by their length. o) Total nucleotide and di-nucleotide composition of the unified peaks. p) Total length of the unified peaks. q) Average and standard deviation of the lengths of unified peaks. |
- Output file with the suffix .cluster.out. This file contains: |
a) Parameters of the specific analysis.
b) Total number of clusters. c) Discrete display of the number of clusters. d) Clusters ordered by their location in the sequence. For each cluster - all the peaks in the cluster. For each peak - its location in the sequence, its length and area. e) Total number of clusters comprised of unified peaks. f) Discrete display of the clusters comprised of unified peaks. g) Clusters comprised of unified peaks ordered by their location in the sequence. For each cluster - all the peaks in the cluster. For each peak - its location in the sequence and its length. |