Vertical ideogramic layout showing relationships between the reference genome Oryza_sativa the target genome Brachypodium_distachyon.
Chromosomes are visually encoded by idegrams and relationships are illustrated by the adjacent track to the right which are dots or bins.


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To Do Tip: Can click on a vertical ideogramic representation of a target genome chromosome to study synteny.

Target Genome
Tracks
orthologous relations syntenic blocks (syntenic regions based on collinearity) homologous relations
Features
repeat_stackbar heatmap
Reference I Genome
Features
rsci
General Viewer Settings
Grid: Ruler:


Data sets

All the analysis is based on transcript annotation of Oryza sativa, of Sorghum bicolor and of Brachypodium distachyon, extracted from PGSB PlantsDB. Oryza sativa data in PlantsDB is based on the TIGR assembly. Transcript annotation is an unspliced sequence which considers the exons, introns and UTRs, for more detailed information please refer to Transcript description.


Methods

Analysis was perfomred using CrowsNests comparative pipeline. For more details please refer to the publication.

Orthologs and Homologs. Similarity searches were done with TBlastx and Blastn using standard parameter settings(version 2.0.12). The output was parsed and filtered for BLAST score, percentage identity and hit length which needed to be above a predefined genome specific threshold. The thresholds were manually derived by analysis across the whole data set. The matches were sorted by the percentage identity multiplied with the hit length and filtered for the best match. Orthologs were derived by calculating BBHs with the requirement of having the same order and direction of BLAST Hsps. A minimum match overlap of 50% was required with a minimum sequence simirality of %70.

Synteny. Syntenic regions, often referred to as syntenic blocks, were derived requireing a minimum of 3 consecutive BBHs allowing a certain number of gaps adjusted by the length of the block. All BBHs which belong to a syntenic block were assigend syn+ and all others were classified as syn-.

Zscore. Using a sliding window a zscore was calculated on the basis of syn+ and syn- along the whole genome.

Features. For information about genetic elements, gene families and all other please refer to the publication.