[Bioc-devel] Best object structure for representing a pairwise genome alignment ?

[Charles Plessy]

Dear Bioc developers,

I am currently analysing pairwise genome alignments with Bioconductor, 
and I represent them with a GRanges object of the first genome, 
containing one element by alignment block, and storing the coordinates 
in the other genome in a metadata column containing another GRanges object.

Something like this.

GRanges object with 36582 ranges and 2 metadata columns:
           seqnames      ranges strand |     score                query
              <Rle>   <IRanges>  <Rle> | <numeric>            <GRanges>
       [1]       S1     162-550      + |       861    XSR:909374-909853
       [2]       S1    833-3738      + |      7238    XSR:910181-913291
       [3]       S1   3769-4212      + |      1165    XSR:913510-913953
       [4]       S1   4246-4381      + |       359    XSR:914134-914275
       [5]       S1   4532-5990      + |      2977 chr2:6694031-6695569
       ...      ...         ...    ... .       ...                  ...
   [36578]      S99 17228-17759      - |       793 chr1:2375870-2376379
   [36579]      S99 16417-16935      - |       632 chr1:2376612-2377077
   [36580]      S99 12370-12759      - |       773 chr1:2379949-2380343
   [36581]      S99   5270-5384      - |       295   chr1:843397-843511
   [36582]      S99   1949-3053      - |      2105   chr1:845358-846326
   -------

Using "Pairwise genome alignment" as a keyword in a search engine, I 
found that the packages CNEr is doing something similar, although it 
uses a dedicated "GRangePairs" object for the purpose.

Before I start to invest time in either direction, I wanted to check on 
that mailing list if there were other solutions already existing, in 
particularly closer to the core packages ?

Have a nice day,

Charles

-- 
Charles Plessy - - ~ ~ ~ ~ ~ ~~~~ ~ ~ ~ ~ ~ - - charles.plessy using oist.jp
Okinawa  Institute  of  Science  and  Technology  Graduate  University
Staff scientist in the Luscombe Unit - ~ - https://groups.oist.jp/grsu
Toots from work - ~ ~~ ~ - https://mastodon.technology/@charles_plessy