how to identify CEN180 repeat?

[xingchang-web]

dear author
When I learn the method of identifing CEN180 reapeat from your article,I have some questions. 1. When you merged contiguous windows, did you re-identify the new kmer or use the kmer obtained in the previous step? 2. How to understand "histogram of the distances between 12-mers"

3. According to me, the N value was the distance between the starting points of two new adjacent highest frequency kmers. Can i got it by this way？Could you draw a schematic diagram if possible？
Thank you very much.
Best
XingChang

[mschatz]

Thanks for your interest. To identify repetitive regions, we consider all possible 12mers that are present. This is first done in fixed length 1kbp windows, but then consecutive windows are merged together into larger regions. The merging doesnt reexamine the 12mers, it just looks at the coordinates. Then once we have identified those regions, we do a follow up analysis to look for periodic repeats. During this part of the analysis, we extract the 12-mer at each possible offset and then look to see where it next occurs. The distances from once occurrence to the next are then displayed as a histogram. Does that make sense? Good luck Mike

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On Fri, Feb 25, 2022 at 9:44 PM xingchang-web ***@***.***> wrote: dear author When I learn the method of identifing CEN180 reapeat from your article,I have some questions. 1. When you merged contiguous windows, did you re-identify the new kmer or use the kmer obtained in the previous step? 2. How to understand "histogram of the distances between 12-mers" [image: image] <https://user-images.githubusercontent.com/67858280/155825501-96927f51-5296-4778-bb3a-f4843caee124.png> 3. According to me, the N value was the distance between the starting points of two new adjacent highest frequency kmers. Can i got it by this way？Could you draw a schematic diagram if possible？ Thank you very much. Best XingChang — Reply to this email directly, view it on GitHub <#3>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABP344DIRQ2XV7WKADXKDTU5A5BJANCNFSM5PL3DW6A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[xingchang-web]

Dear author
Thank you for your reply. But I still have some questions. Compared with Arabidopsis, if there are still millions of SNPs and InDels in the genome , can I use your method to identify monomer sequences? Whether the length of the monomer sequence is different in different species? Is there a range for the length of the monomer?
Best
XingChang

[mschatz]

There is a lot of variability in centromere sequences across species. The CEN180 sequence in Arabidopsis was first recognized some 20 years ago ( https://www.science.org/doi/10.1126/science.286.5449.2468), but rice has a characteristic 155bp sequence CentO ( https://academic.oup.com/plcell/article/14/8/1691/6009797) and the human centromere repeat is 171bp ( https://www.biorxiv.org/content/10.1101/2021.07.12.452052v2). This paper describes these results across 282 species and describes a pipeline that can be used for general analysis: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-1-r10 I'd recommend you explore this and related works since our approach was specialized for Arabidopsis Good luck! Mike

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On Tue, Mar 1, 2022 at 9:10 AM xingchang-web ***@***.***> wrote: Dear author Thank you for your reply. But I still have some questions. Compared with Arabidopsis, if there are still millions of SNPs and InDels in the genome , can I use your method to identify monomer sequences? Whether the length of the monomer sequence is different in different species? Is there a range for the length of the monomer? Best XingChang — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABP344FSKDED5BZO6RT5STU5YQL3ANCNFSM5PL3DW6A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.Message ID: ***@***.***>

[xingchang-web]

Dear author
Thank you so much for your help!
Best
XingChang