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Sequence format
Fasta
Plain text
Fasta format: Each sequence starts with a header indicated by “>” symbol. Multiple text lines between headers will be treated as one sequence.
Plain text: Headers are optional. If multiple sequences are provided they should be placed each on a separate line. Lines starting with “>” will be ignored.
In both formats, letters A, C, G, T in lower or upper case will be recognized as Adenines, Cytosines, Guanines, and Thymines respectively;
all other symbols, including blanks, will be treated as “mixed-sequence” DNA (see Methods for detail).
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Copy and paste sequences for analysis in the text box below
Sequences should be no shorter than the size of the
window for nucleosome-positioning score calculations (see below)
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OR
Submit a file containing sequences for analysis
This is a preferred option if the number of sequences
is large |
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OR
Submit an example sequence
(sea urchin 5S rDNA) |
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Calculate average and standard
deviation
If selected, position-wise averages and standard deviations will be
calculated over all the input sequences. This option should be used
only for aligned input sequences.
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Random sequences:
Adding random sequences will increase the computation time
If selected, a specified number of random sequences of the same dinulceotide
content will generated for each of the sequences provided for the analysis.
The DNA deformation energy and nucleosome-positioning scores for the
random sequences will be reported along with the scores for the input
sequences.
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Number
of sequences
(range 2 -1000)
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Template:
Symmetrical
Template selection
Eight structural templates are available (see User Manual for detail).
The default tepmlate is based on the best-resolved nucleosome structure
NCP147 (PDB_ID 1kx5).
Symmetrical template: the template with the structural parameters
symmitrized relative to the dyad (see Methods for detail).
Complete/Partial template: only a fragment of the complete template
will be used for the threading calculations if partial templte is selected.
The fragment is selected symmetrically relative to the dyad of the corresponding
template and therefore, the length of the partial template should be
odd for the NCP147 and NCP145 structures and even for the NCP146 structures.
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Template size (in base pairs)
Less or equal to complete template size (147, 146, or 145 bp)
ODD number for ncp147 and ncp145 templates
EVEN number for ncp146 templates
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Template orientation relative to sequence
‘Direct’ orientation corresponds to the orientation of the structural
template as it appears in published pdb-file. ‘Reverse’ orientation
corresponds to the template rotated by 180 degrees relative to its structural
dyad (see Methods for detail). If options ‘Average’ or ‘best of
two’ are selected, the average or the lowest energy score for the
direct and reverse template orientations will be reported.
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Window size for nucleosome-positioning
score calculations (in base pairs) :
Window size specifies how many neighboring positions of the template
on the sequence will be used to calculate the nucleosome positioning
score for a given position (see Methods for detail).
No less than the selected template size. Recommended window size: Template size + 18 bp
ODD number for ncp147 and ncp145 templates; EVEN number for ncp146 templates
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