Skews generator

Skews from custom sequences

Compute GC-, AT-, KETO- and oligo-skews from a custom sequence. The input sequence is scanned with a sliding window and the requested parameter is calculated for each window, then plotted in a graph.

Parameters

Fill in the data to analyse, then run the computation.

Name of sequence :

Copy sequence in the textarea below (up to 5,000,000 bp):

GGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGCGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGGGGGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGCGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGGGGGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGCGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGGGGGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGCGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGGGGGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGCGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGGGGGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGCGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGGGGGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGCGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGGGGGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGCGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGGGGGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGCGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGGGGGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGCGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGGGGGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGCGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGGGGGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGCGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGGGGGGGAGTGAGGGGAGCAGTTGGGCCAAGATGGCGGCCGCCGAGGGACCGGTGGGCGACGCGG

Window size :

bases(100-50000)

Show G+C%

Show GC

Show AT-skew

Show KETO-skew

Show oligo-skew for

Window size :

Show subsequence from

Description

Skews from custom sequences

To compute skews, the input sequence is scanned with a sliding window, and the requested parameter is calculate for each window. The data is shown in a graph.

G+C %

The porcentaje of G+C is computed

GC-skew

For each window, (G-C)/(G+C) is computed, where G and C are the number of ocurrences for each nucleotide

AT-skew

For each window, (A-T)/(A+T) is computed, where A and T are the number of ocurrences for each nucleotide.

KETO-skew

For each window, (G+C-A-T)/(G+C+A+T) is computed, where A, C, G and T are the number of ocurrences for each nucleotide.

Oligo-skew

For each window, frecuencies for all nucleotides with selected length is computed. Those frecuencies are compared to frecuencies obtained from the complete sequence. When comparing both frecuencies, global distance is computed, as described by Almeida et al. (2001).

Text taken from biophp.org.