MS4--Multi-Scale Selector of Sequence Signatures: an alignment-free method for classification of biological sequences.

Background: While multiple alignment is the first step of usual classification schemes for biological sequences, alignment-free methods are being increasingly used as alternatives when multiple alignments fail. Subword-based combinatorial methods are popular for their low algorithmic complexity (suffix trees ..

Comparing sequences without using alignments: application to HIV/SIV subtyping.

Background: In general, the construction of trees is based on sequence alignments. This procedure, however, leads to loss of informationwhen parts of sequence alignments (for instance ambiguous regions) are deleted before tree building. To overcome this difficulty, one of us previously introduced a new and rapid algorithm that calculates dissimilarity matrices between sequences without preliminary alignment.

The new variant of the Creutzfeldt-Jakob disease accounts for no relative increase of the Creutzfeldt-Jakob disease mortality rate in the United Kingdom; this fits ill with the new variant being the consequence of consumption of food infected with the agent of Bovine Spongiform Encephalopathy.

Background: A new variant of Creutzfeldt-Jakob disease was described in the United Kingdom. It is often claimed that it is caused by consumption of food infected with the agent of bovine spongiform encephalopathy. However, this remains open to question because the number of cases of the variant is, at the present time, less than would be expected from a major food-borne source.

HIV-1 and HIV-2 LTR nucleotide sequences: assessment of the alignment by N-block presentation, "retroviral signatures" of overrepeated oligonucleotides, and a probable important role of scrambled stepwise duplications/deletions in molecular evolution.

Previous analyses of retroviral nucleotide sequences, suggest a so-called "scrambled duplicative stepwise molecular evolution" (many sectors with successive duplications/deletions of short and longer motifs) that could have stemmed from one or several starter tandemly repeated short sequence(s). In the present report, we tested this hypothesis by focusing on the long terminal repeats (LTRs) (and flanking sequences) of 24 human and 3 simian immunodeficiency viruses. By using a calculation strategy applicable to short sequences, we found consensus overrepresented motifs (often containing CTG or CAG) that were congruent with the previously defined "retroviral signature.