Hi there,
I'm comparing the arrangement of a gene complex across different species to try and find clues about its evolutionary history. In some cases genes appear to have jumped around and switched positions, but I do not know if this is the result of recombination, or due to the orientation in which the chromosome has been assembled?
I'm taking data from the NCBI genome browser using ref seq chromosome level assemblies in each case. Does anyone know if there a standard direction that homologous chromosomes have to be uploaded in?
I imagine this is perfectly possible to do if you consider the positions of conserved genes at each end of the chromosome, but I would rather not have to do this myself if I know that it has already been accounted for...
Thanks,
Jake
Yes, there is a standard orientation for chromosomes to be assembled in most genome sequencing and assembly projects. Chromosomes are typically assembled with a consistent orientation known as the "forward" or "+" orientation. In this orientation, the DNA sequence is aligned from the 5' end (start) to the 3' end (end) of the chromosome. This convention ensures consistency in the representation of genomic information across different studies and facilitates comparisons between different genomes.
The forward orientation is determined based on the directionality of DNA replication during genome sequencing and assembly processes. The DNA strands are typically sequenced in both directions, and the resulting reads are then aligned and assembled into contigs, which are further scaffolded to construct chromosome-level assemblies.
It's worth noting that in some cases, certain regions or genes within a chromosome may be inverted or have a reverse orientation due to specific biological features, such as gene rearrangements or evolutionary events. However, the majority of the chromosome is assembled and represented in the forward orientation to maintain consistency and standardization in genome research.
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