CpGcluster

CpGcluster uses only integer arithmetic, thus being a fast and computationally efficient algorithm able to predict statistically significant clusters of CpG dinucleotides. Another outstanding feature is that all predicted CGIs start and end with a CpG dinucleotide, which should be appropriate for a genomic feature whose functionality is based precisely…

Bioinformatics

La biología computacional, biocomputación o bioinformática es un campo relativamente reciente. Aunque es difícil fijar exactamente su origen, se trata de una disciplina científica con un rapidísimo desarrollo, basado fundamentalmente en los extraordinarios avances hechos en secuenciación genómica y en las técnicas para la elaboración de mapas genéticos, además de…

IsoFinder

Isochores are long genome segments homogeneous in G+C. The algorithm IsoFinder [1] is able to predict isochores at the sequence level. Most of the IsoFinder isochores show correlation with biological features such as gene density, SINE and LINE densities, recombination rate or SNP variability. The reliability of this algorithm in…

DNAkeywords

Relevant words in literary texts (key words) are known to be clustered, while common words are randomly distributed. Given the clustered distribution of many functional genome elements, we hypothesize that the biological text per excellence, the DNA sequence, might behave in the same way: k-length words (k-mers) with a clear…

DNA segmentation

Segment The analysis of sequence correlation structure, in both the spatial and the frequency domains, resulted in the finding of short-range and long-range correlations in nucleotide sequences, thus uncovering a complex fractal structure for DNA. Sequence structure can be adequately revealed through segmentation algorithms. One of these, conceptually simple and…

DNA methylation

DNA methylation is an epigenetic mark involved in embryonic development, transcription, chromosome stability and genomic imprinting. Aberrant methylation is implicated in the appearance of several disorders such as cancer, immunodeficiency or centromere instability. NGSmethDB is a dedicated database for the storage, browsing and data mining of whole-genome, single-base-pair resolution methylomes.…