The output is dual, provided in the form of text files as well as graphical in the form of SymCurv and nucleosome position plots. Graphical output is disabled for sequences longer than 10Kb for speed purposes.
The symmetry of curvature is a property of DNA sequence with special attributes. Unpublished results suggest a strong tendency for nucleosome-forming sequences to have high values of SymCurv. At the same time, SymCurv is able to capture sequence constraints, which are related to structure in genomic regions where a functional predicted role is not supported by sequence conservation. SymCurv raw values may thus serve as an interesting structural aspect of a DNA sequence.
The raw SymCurv values are provided as a tab-delimited file. This contains the name of the sequence at the first field, followed by the relative coordinates in the second field. These are calculated relatively to the initial offset coordinate provided at the header of the sequence (here 1). Fields 3 and 4 in the tab-delimited file contain the SymCurv values as calculated with the use of two alternative geometrical parameters. Field 3 refers to SymCurv values obtained with the use of nucleosomal-specific parameters (nuc), while field 4 to the ones obtained with the use of DNaseI-specific parameters. (For more information on this, please check the SymCurv Documentation). Raw SymCurv values fall in a range between 0 and 100.
sacCer1_ensGene_YMR244W 58 0 0
sacCer1_ensGene_YMR244W 59 0 0
sacCer1_ensGene_YMR244W 60 0.0465047685983504 0
sacCer1_ensGene_YMR244W 61 0 0
sacCer1_ensGene_YMR244W 62 0 0
sacCer1_ensGene_YMR244W 63 0 0.0295858067463842
sacCer1_ensGene_YMR244W 64 0 0
sacCer1_ensGene_YMR244W 65 0 0
sacCer1_ensGene_YMR244W 66 0 0
sacCer1_ensGene_YMR244W 67 0 0
sacCer1_ensGene_YMR244W 68 0 0.402540082453594
sacCer1_ensGene_YMR244W 69 0 0
sacCer1_ensGene_YMR244W 70 0 0
sacCer1_ensGene_YMR244W 71 0 0
sacCer1_ensGene_YMR244W 72 0.262897808372804 0
sacCer1_ensGene_YMR244W 73 0 0
sacCer1_ensGene_YMR244W 74 0 0
sacCer1_ensGene_YMR244W 75 0 0
The SymCurv raw values are used in deducing the predicted nucleosome positions on the sequence of interest.
The user can obtain two files containing the predicted nucleosome positions based on the two alternative geometrical parameter files (see above). Files are in gff (general file format)
sacCer1_ensGene_YMR244W SC_call_nuc SC_nucleosome 88 234 3.78776165891352 . . .
sacCer1_ensGene_YMR244W SC_call_nuc SC_nucleosome 553 699 1.91633774580324 . . .
sacCer1_ensGene_YMR244W SC_call_nuc SC_nucleosome 743 889 1.9580759678685 . . .
sacCer1_ensGene_YMR244W SC_call_dnase SC_dnase 66 212 1.65028971344348 . . .
sacCer1_ensGene_YMR244W SC_call_dnase SC_dnase 366 512 1.93077567379365 . . .
sacCer1_ensGene_YMR244W SC_call_dnase SC_dnase 749 895 10.6447513336063 . . .
Each line in the gff file (general file format) corresponds to one predicted nucleosome. The first column contains the sequence name. Start and end of the nucleosome are given in columns 4 and 5. These are given with reference to the offset coordinate provided at the header of the fasta sequence, submitted initially. Each line also contains a score (given at column 6), whose range is 0-100. This is the SymCurv score for the center of the predicted nucleosome.
Differences in the two profiles are representing nucleosomes, which are predicted to have a tendency for remodelling. Since DNaseI hypersensitive sites are known to be regions of open-chromatin and increased transcriptional activity we hold the obtained positions to be the ones reflecting a more active, dynamic state of chromatin conformation, thus we choose to refer to the "nucleosome" predictions as corresponding to "stationary" and the "DNaseI" ones to "dynamic". Nucleosomes existing in the "nucleosome" set and absent in the "DNaseI" one are likely to be evicted during activation of the chromatin, while in the opposite case nucleosomes are predicted to be appearing during chromatin activation (See SymCurv Documentation for more information).
Raw SymCurv profiles are provided as bar-plots in a single clickable jpg file, available for download.
Both sets of nucleosome predictions are also provided in a pdf plot, which the user can download by clicking on the corresponding link. The plot has been created with the use of gff2ps.