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While aligning a 19nt-long sequence to the human reference genome (hg38) using `bwa aln`, I get the unexpected results to get less reported alignments when using 6 mismatches instead of 5.
My toy e…
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If I accidentally merge Greek words that have already been aligned (or I change my mined), It would be nice if when I unmerged them the original alignments would remain rather than all of the GL words…
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I found that the positions of all images in the img-outglobal-positions-0.txt file are integers.
I would like to ask if it is possible to choose sub-pixel registration like Fiji.
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Currently sort -n merely sorts by the probeid. However, many programs output multiple alignments per read (splicing, blat, etc.). For these kinds of paired-end alignments, using sort -n will typic…
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The tool currently supports target to target replacement suggestions only. To perform source to target replacements, an alignment model is run and replacements are performed as a pre-processing step. …
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## Expected Behavior
I was testing foldseek multimer search on these two structurally similar PDBs obtained from RCSB PDB (also tried PDB-redo). However, the results are not returned as the files a…
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Hi Philip,
Just playing around with large SW alignments and have noticed that the maximum alignment length is capped due to i16 constraints: https://github.com/philipc/gkl-rs/blob/9eec44205839fc9e7…
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I've been trying to run GA on my custom structure, `Organism`, but it's giving the following error:
```julia
result = Evolutionary.optimize(
fitness,
() -> init_organism("msa_dat…
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Hello,
Is it possible for PsiClass to be executed on long-reads generated from PacBio and/or Nanopore? If not, is it possible to make quick modifications to the code to adapt to long reads?
Than…
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Hi, I am working with Nanopore direct-RNA sequencing and found your tools really useful. However, while I was trying to use your BamSlam script to generate some summaries and figures for the alignment…