Features of Cinteny Server

The server allows different types of queries related to finding synteny and measuring genome rearrangement.

Whole Genome Analysis

This query finds synteny regions and reversal distance for the genomes selected, taking two at a time. The results displayed include the reversal distance, number of synteny blocks and a synteny map. The synteny map shows one genome as composed of chromosomes of the other genome. This allows quick visualization of genome rearrangment. Clicking on a synteny map shows the synteny regions in detail in synbrowse.

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Chromosome v/s chromosome Analysis

This query allows one to compare chromosomes of two genomes. This is useful to study the evolution of chromosome, for example, chromosome X of human with chromosome X of mouse. In this analysis, only the homologous genes present in each chromosome are used for the analysis. The output page shows the synteny blocks and the reversal distance.

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Find Synteny Around a Marker

Often it is of interest to find out if a gene of interest is converved in different genomes and if its neighborhood is conserved too. With this query, you may select a genome and enter a gene name. The search is case in-sensitive.

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Using Multiple Genomes

Cinteny offers the option of using multiple genomes to define a set of common, evolutionarily conserved markers (e.g. orthologs identified in all genomes included in the analysis, as specified by the user). This approach yields a natural coarse-graining, in which only the most conserved markers are taken into account when identifying syntenic blocks and computing reversal distances.

Finding synteny blocks and the reversal distance typically involves identifying genes (or sequence tags) that are shared by the two species of interest. For example, the synteny between human and mouse may be analyzed using 15,645 orthologs, as identified by Homologene (NCBI, 2005). Alternatively, multiple organisms may be used, in order to define a reduced set of markers common to multiple species. For example, one may use a subset of 6,424 orthologs common to human, chimpanzee, dog, mouse and rat genomes, in order to find synteny between human and mouse or other pairs of genomes.

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