FineStr HELP

This is an on-line help file for the sequence directed nucleosome mapping using FineStr(version 1.00). FineStr allows you to submit a genomic sequence and to receive a prediction of a general map of nucleosome positions on it, using a probe based on the DNA bendability matrix of C. elegans that we describe in (Gabdank et al. 2009).

Nucleosome Mapping Probe

The probe size is 117 bases (116 dinucleotides) that corresponds to the size of DNA-histone contact area. The probe was constructed by extension of earlier published DNA bendability matrix.

Sequences supported

FineStr supports input of single or multiple Fasta format sequnces. Currently the server is limited to sequnces of a total length of up to 10000 nucleotides. The sequnce minimum length should be above 117 nucleotides to enable the use of the probe that is 116 dinucleotides long.
Each sequence starts with a unique header indicated by ">" symbol. Letters A, C, G, T in lower or upper case will be recognized as Adenines, Cytosines, Guanines, and Thymines respectively. Letters N or X will be treated as unknown or unspecified nucleotides.

Files supported

FineStr supports input of a text file containing single or multiple Fasta format sequences. Currently the server is limited to files under 50 kb size.

Nematode pattern universality

Although, in principle, every genome would have its own matrix of bendability, influenced by different factors (e.g. the species specific nucleotide composition), we obtained strong evidence suggesting the nematode pattern to be close to the universal one. Our latest sequence-based data1 and physics of DNA bending2 attest to the universality of the pattern found. Identical sequence patterns are derived by minimization of DNA unstacking2, as well as by merger of two binary patterns (RR/YY and SS/WW), by matching all patterns suggested since 1980, and by reconstruction via fusion of most frequent oligonucleotides in eukaryotes1.

1. Trifonov E.N. Nucleosome positioning by sequence, state of the art and apparent finale. J. Biomol. Struct. Dyn., in press.
2. Trifonov E.N. Base pair stacking in nucleosome DNA and bendability sequence pattern J. Theor. Biol., in press.

Change log

October 2009
- Updated the probe file.
December 2009
- Updated the help file, regarding the universality of the pattern.


For any assistance please contact Idan Gabdank at gabdank@cs.bgu.ac.il