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As I've been diving further into this package, I am realizing that this isn't exactly what I thought it was. Bioalignments.jl is for aligning two sequences in string format. Do we have any julia packages for aligning fastx files together? We could convert the fastx files to strings and then use Bioalignments, but I wasn't sure if the package was optimized for working with such big strings. What have you done in the past? Do you usually just use a command line tool in a bash script? |
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Preview at https://biojulia.github.io/BioTutorials/29 |
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Preview at https://biojulia.github.io/BioTutorials/29 |
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@kescobo I have finished the rough draft of my overview of the BioAlignments package. However, before wrapping up the tutorial, I would love some insight on the above comment/the best example to display (whether that's an alignment between some strings, or actual fastx files). |
| - GlobalAlignment: global-to-global alignment | ||
| - `GlobalAlignment`: global-to-global alignment | ||
| - Aligns sequences end-to-end | ||
| - Best for sequences that are already very similar |
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Might be nice to give examples here - an example here might be you have a particular gene from two closely related bacteria, or you're comparing alleles of a gene between two individuals.
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Preview at https://biojulia.github.io/BioTutorials/29 |
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Preview at https://biojulia.github.io/BioTutorials/29 |
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Hi @kescobo you have already approved this PR. However, I made a lot of updates since the draft PR was created. I would love a quick sanity check of the final PR before merging if you get a chance. Thanks! |
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Preview at https://biojulia.github.io/BioTutorials/29 |
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Preview at https://biojulia.github.io/BioTutorials/29 |
| `BioAlignments` implements pairwise alignment. | ||
| Pairwise alignment differs from multiple sequence alignment (MSA) because | ||
| it only aligns two sequences, while MSAs align any number of sequences. | ||
| There is not currently a MSA package in Julia. |
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Jakob said this, can Kevin confirm?
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Explaining how to use BioAlignments.jl and providing some examples!