Due to the data field size limitations imposed by browsers on various platforms, there exists a maximum limit of 29 kb for PC browsers. To overcome this limit please use the Sequence File Upload form.
The Sequence Upload Form lets you select a sequence file via your web browser and allows you to upload it to the MAR-Finder server where it is analyzed by our CGI program. This form eliminates the need for copying and pasting your sequence data, and also overcomes the field file size limits of some browsers.
- Origin of Replication:
It is known that DNA replication is associated with the nuclear matrix. It has also been demonstrated that nuclear matrix attachment sites, homeotic protein recognition and binding sites and the origins of replication share the ATTA, ATTTA and ATTTTA motifs. This implies that differential activation of origins of replication (important for development) are regulated while part of the nuclear matrix.
Some matrix attachment regions have been characterized by T-G rich spans. These regions are abundant in the 3'UTR of a number of genes, and may act as signals at the recombination sites, e.g. immunoglobulin genes.
- Curved DNA:
Intrinsically curved DNA has been identified at or near several matrix attachment sites. Curved DNA is also considered to play an important role in nuclear processes that involve the interaction of DNA and proteins, such as recombination, replication, and transcription. Optimal curvature is expected for sequences with repeats of the motif, AAAAn7AAAn7AAAA as well as the motif TTTAAA.
- Kinked DNA:
Kinked DNA has generally been associated with the presence of copies of the dinucleotide TG, CA or TA that are separated by 2--4 or 9--12 nucleotides.
- Topoisomerase II Recognition:
Topoisomerase II binding and cleavage sites are concentrated at the sites of nuclear attachment. Selecting this rule will use both vertebrate and Drosophila topoisomerase II consensus sequences.
Many MARs contain significant stretches of AT-rich sequences. It has been suggested that the simple occurrence of isolated AT-rich regions is not sufficient to cause matrix association. Several such regularly spaced motifs are required for matrix association. Such a periodicity was considered while formulating this rule.
- Window Width:
Window Width is 1000.
- Slide Distance:
Slide Distance is 100 units.
- Cut-Off Threshold:
The MAR-potential values are normalized to fall between 0 and 1. This parameter specifies the minimum normalized potential above which there is a high likelihood the underlying region has a MAR site. The default has been set to '0.6'.
A true MAR will be characterized by a run-length of high potential values. In other words, if the average span of a MAR is 650 bp, we should expect to see successive high potential values in an average run length of 1000-650/100, or 3 successive window readings. This is also the default value.
- Do Not Clip Peaks:
The default is set to not clip peaks.
- Clip Peaks:
Sometimes a significantly high value of MAR-potential can reduce the values of other peaks during the normalization process. This may happen in spite of the other peaks being statistically significant. In order to avoid this from happening, a user may choose to saturate the largest potential value and thus retain sensitivity to the relatively lower values. If the user chooses to clip the default clipping parameter will restrict the largest peak to 0.5 of the raw value.
- Consensus Motif:
TCTTTAATTTCTAATATATTTAGAA (Kohwi-Shigematsu's lab, JBC, 270:23239-23242).
- ATC Rule:
ATC Rule (a stretch of 20 or more occurrences of H, i.e. A or T or C). The ATC Rule was used in the analysis of Rice A1-Sh2 region by Dr. Alexander Tikhonov at Purdue University. Research is underway to establish its universal validity.
- Average Strength:
Average strength is defined as the potential per window of the MAR scanning process. The average is computed by considering all the contigous windows that have a potential higher than the threshold.
- Integragted Strength:
Integrated Strength is defined to be total MAR potential summed over the entire span of the deteced MAR. For example, if the MAR has an average strength of 0.6 and spans 2000bp, its integrated strength would be 1200. This paramters provides an estimation of the span of the MAR activity, where the integrated potential is proportional to the MAR span. (A localized MAR activity would be characterized by a high average strength, but a low integrated strength.)