Question

BLAST-like alignment of a DNAString to a BSgenome?

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Charles Plessy ▴ 180

@charles-plessy-7857

Last seen 13 months ago

Japan

Hello,

I am looking for a way to align a sequence stored in a DNAString object to a BSgenome object with similar speed as with BLAST or long-read aligners. The sequence might be matching a repeated region multiple times, and checking for that is the reason why I would like to do the alignment. Since I find the sequence of interest during an interactive R session, I would prefer to use Bioconductor functions to run the alignment.

I found the previous question https://support.bioconductor.org/p/53668/ which suggested that there was only matchPattern available, which more precise and therefore limited to cases with at most ~15 mismatches. I have not found alternative, but if I missed something, please let me know !

-- Charles

Alignment Genome • 1.2k views

ADD COMMENT • link 3.1 years ago Charles Plessy ▴ 180

score 0 · Answer 1 · 2021-10-17

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Hervé Pagès 16k

@herve-pages-1542

Last seen 13 hours ago

Seattle, WA, United States

Hi Charles,

One alternative I'm aware of is annotate::blastSequences() but I've no experience with it.

Best,

H.

ADD COMMENT • link 3.1 years ago Hervé Pagès 16k

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Thanks Hervé. annotate::blastSequences() sends jobs to the NCBI server, so that is not exactly what I was looking for. I searched again and found that the CNEr package had some functions (CNEr::blatCNE and CNEr::lastz) that utilise the 2bit extdata of BSgenome packages. The functions are devoted to a specific use case, so I can not use them directly, but it may be a good start.

ADD REPLY • link 3.1 years ago Charles Plessy ▴ 180