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baoxingsong / AnchorWave

Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation
MIT License
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How should I align chromosome regions between distantly evolutionary species? #48

Open Rafaelsoler13 opened 1 year ago

Rafaelsoler13 commented 1 year ago

Hello,

I am currently working on a comparative genomics project and I would like to align chromosome regions between distantly evolutionary species, specifically chicken, mouse, and human. I came across your tool and its tutorial, but it seems to focus primarily on aligning full genomes rather than specific chromosome regions.

I am wondering if your tool supports the alignment of chromosome regions across these species, allowing me to identify conserved regions and study the genomic rearrangements. If it does, I would greatly appreciate some guidance on how to utilize the tool for this purpose, or any specific commands or options that enable the alignment of chromosome regions between distantly related species.

Best regards,

Rafael

baoxingsong commented 1 year ago

Hi, Rafael,

I am not sure how large is the specific region. If it is small (say less than 200Kb), you could run anchorwave ali -w 200000. If it is much larger, you may need to align the whole genome and extract the alignment result for this specific region.