The analysis of the frequency and distribution of words (oligonucleotides) in DNA sequences has a long tradition. Recently, several novel tools have been generated to perform quite complex word-based analyses, such as oligonucleotide profiling of chromosomes or whole genomes. However, these tools are not readily available.
We introduce UVWordweb, an integrated platform for different types of word-based DNA sequence analyses. UVWordweb includes all the programs recently generated by our group to perform oligonucleotide profiling, plus other classical kinds of analyses (e. g. chaos game representation, masking of sequences, motif searches, etc.). All of them are accessible through a user-friendly web page (http://UVWordweb.uv.es/). Results can be obtained in a very short time (typically a few seconds), given that the speed of standard analyses range from 3 to 140 Mb/second on standard PC computers. In addition, and to facilitate the most common searches, the chromosomes of 13 fully-sequenced eukaryotic model species are preloaded. Several types of graphical outputs make the results easily evaluable.
Its speed, simplicity of use and the generation of self-explaining graphical outputs make UVWordweb the program of choice for users interested in performing word analyses in DNA sequences. In addition to their interest for researchers, these web pages can also be used by students that want to better understand the basic features of these sequences.
Gallach M, Arnau V, Marín I. Global patterns of sequence evolution in Drosophila. BMC Genomics, 2007, 8:408. Download: PDF
Arnau V, Gallach M, Marín I. Fast comparison of DNA sequences by oligonucleotide profiling. BMC Research Notes 2008, 1:5 Download: PDF - Supplementary
Gallach M, Arnau V, Aldecoa R, Marín I. A sequence motif enriched in regions bound by the Drosophila dosage compensation complex. BMC Genomics 2010, 11:169. Download: PDF
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Teoría, Bioinformática y Computación