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dna samples of > 140  000 named organisms can be found , for example , in genbank .
the characteristics of these sequences have been extensively studied , and extracted information is often interpreted in terms of evolution or systematic molecular biology .
it quickly became obvious that the set of oligonucleotide frequencies was species specific ( 26 ) .
on the one hand , the genomic signatures of species differ from one another , and , on the other hand , the majority of genome segments within a species have comparable signatures . as a consequence , each species can be assigned a dna style that can be derived from most of its available dna fragments .
the methodology that we have developed thus makes it possible to study and compare a great number of sequences and species , inasmuch as the calculation of a signature on a laptop computer requires < 1 s per million nucleotides . the genomic signature is visualized as a parametric image using the  chaos game representation algorithm ( 3,5,8,1114 ) .
our experience with genomic signatures shows that the comparison of four - letter word signatures offers a good trade - off between accuracy of classification , usual size of dna fragments and computer load ( 9,15 ) . in our hands ,
comparison of signatures is achieved by means of the euclidian metric in a space with 256 dimensions ( there are 256 different 4-letter words ) . of course , other methods for comparison of signatures are available .
they often provide slightly different results [ see refs ( 4,8,16,17 ) for some other measures of dissimilarities ] .
it must be pointed out that comparisons of dna style do not require homologous sequences and almost any dna segment is eligible ( 4,9 ) .
in fact , the species - specific dna style concept motivates and justifies most of the works dealing with the genomic signature , including , for example , assignment of genomic fragments ( 4,18 ) , taxonomic / phylogenetic analyses ( 15,17,19 ) and detection of horizontal transfers ( hts ) ( 20,21 ) .
some of the abnormal patterns in a genome may be considered to result from hts .
numerous methods relying on a gene 's nucleotide or oligonucleotide composition for the detection of hts are available ( 2232 ) . among them , hidden markov models ( hmms ) and wavelet transforms are two of the efficient approaches in use for detecting and characterizing original motifs and patterns .
many other applications are emerging , such as the characterization of unknown sequences , the quality control of sequencing and pre - processing for homologous sequences screening .
a web service ( ) has recently been made available for the comparison of tetranucleotide usage patterns in dna sequences ( 33 ) .
it comes with pre - computed tetranucleotide usage patterns for 166 prokaryote chromosomes as a source for limited data mining .
. parts of genstyle were made accessible to the bioinformatics community through our site ( ) starting in 1999 , after the publication of the seminal paper describing the concept and its usefulness ( 3 ) .
the sequence analysis toolbox is made for 
 identification of the origin of short dna fragments .
this feature is useful , for example , for the recognition of rare and/or slow growth organisms ( sequences usually hard to characterize).detection of  atypical areas in a genome , in particular the detection of hts ( and potential donors ) .
the closest species ( from the genomic signature point of view ) of an atypical dna segment give clues about the donor in the case of putative hts ( under implementation).building of taxonomic and phylogenetic trees .
distance between signatures remains to been established as a reference for phylogenetic studies , but several recent and interesting results have shown its potentially great value ( 15,17 ) . in particular , our current work with corona viruses is very promising with this respect .
this feature is useful , for example , for the recognition of rare and/or slow growth organisms ( sequences usually hard to characterize ) .
atypical areas in a genome , in particular the detection of hts ( and potential donors ) . the closest species ( from the genomic signature point of view ) of an atypical dna segment
give clues about the donor in the case of putative hts ( under implementation ) .
distance between signatures remains to been established as a reference for phylogenetic studies , but several recent and interesting results have shown its potentially great value ( 15,17 ) . in particular , our current work with corona viruses is very promising with this respect .
there is a large genomic signature database behind genstyle that greatly enhances its power and scope .
the full set of genbank sequences , stored by species , is available for signature studies .
the genstyle companion genomic signature database handles 170  000 species and unspecified organisms ( > 2  000  000 dna sequences ) .
it is updated on a regular basis , using the bimonthly releases issued by genbank .
this makes it possible to work online on the whole set ( or part of it ) of genbank nucleotide sequences belonging to one or several species .
the user 's sequences ( fasta format , eventually grouped into a single text file , zipped or not ) can be uploaded through the uploader.sequence filters toolbox .
although many sequences can be uploaded to a given workspace , it may be interesting to work on selected subsets .
several tools are available for this task , including selection of dna type and size of sequences.sequence analysis toolbox .
if several sequences are analysed together , a distance matrix ( euclidean metric , phylip format ) is provided to build taxonomic / phylogenetic trees ( 8).searching for species with similar dna signatures in the genstyle companion database.observation of similarities ( and differences ) between signatures by principal components analysis ( pca ) ( 34 ) . 

online versions of additional tools already in use in our lab are currently under development .
they include navigation along genomes by means of local signatures ( for ht detection , for example ) , visualization of similarities between local signatures along several genomes and taxonomic trees . sequence collector toolbox .
the user 's sequences ( fasta format , eventually grouped into a single text file , zipped or not ) can be uploaded through the uploader .
although many sequences can be uploaded to a given workspace , it may be interesting to work on selected subsets .
several tools are available for this task , including selection of dna type and size of sequences . sequence analysis toolbox .
if several sequences are analysed together , a distance matrix ( euclidean metric , phylip format ) is provided to build taxonomic / phylogenetic trees ( 8) . searching for species with similar dna signatures in the genstyle companion database .
observation of similarities ( and differences ) between signatures by principal components analysis ( pca ) ( 34 ) .
it demonstrates how the origin of a small dna sequence can be looked for in the genstyle companion database . briefly
, the sequence of interest has to be pasted into the appropriate field of the demonstrator tool ( figure 1a ) .
the sequence signatures for oligonucleotides ( words ) 19 nt long are subsequently calculated , oligonucleotide counts are obtained ( figure 1a ) and signatures are displayed ( figure 1b ) .
distances to the sequence of interest are expressed in an arbitrary unit ( au ) .
it can be seen that the sequence of interest belongs to the sars virus ( d = 11 ) and that the closest species are pedv and ptgv corona viruses .
although this procedure seems to mimic blast / fasta functions , it is quite different in nature . similarities between sequences can be observed even when they are not homologous . as a consequence
, the origin of a sequence can be obtained once the dna material characterizing the genomic signature of the species of origin is available ( typically 2000 nt ) .
genstyle ( ) is a workspace designed for the characterization and classification of nucleotide sequences . 
 based on the genomic signature paradigm , genstyle focuses on oligonucleotide frequencies in dna sequences . 
 users can select sequences of interest in the genstyle companion database , where the whole set of genbank sequences is grouped per species , or upload their own sequences to work with . 
 tools for the exploration and analysis of signatures allow ( i ) identification of the origin of dna segments ( detection of rare species or species for which technical problems prevent fast characterization , such as micro - organisms with slow growth ) , ( ii ) analysis of the homogeneity of a genome and isolation of areas with novel functionality ( horizontal transfers for example )  and ( iii ) molecular phylogeny and taxonomy .