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Hello, I saw your dataset introduction and ran your code. First, I confirmed that, according to the information I understand, your method is actually based on the smiles-protein sequence as input, so …
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Add the smith waterman similarity, and possibly it's variant smith-waterman gotah.
https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm
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I'm trying to do local alignments to find fixed regions in amplicon sequencing.
I think I have the same problem [as documented in SO here](http://stackoverflow.com/questions/35874826/biopython-local…
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Clean up the description, query, attributes by separating connected words and some other issues.
Add new similarity features:
1. Jaro distance.
2. Normalized compression distance.
3. Smith-Wate…
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I was wondering if how DeepVariant performs on short tandem repeats and small inversions has been characterized?
I imagine small inversions aren't a problem, but short tandem repeats might be.
…
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Coming from https://gatkforums.broadinstitute.org/gatk/discussion/9358/gatk-runtime-error-read-max-length-must-be-0-but-got-0-with-1000g-bam#latest. There seems to be a bug somewhere in the implement…
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smith-waterman alignment algorithm needs to be implemented for local alignment.
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Hi,
First of all I would like to thank you for your hard work – I really do appreciate it.
I have called variants using deepvariant v0.7.1 and GATK (4.0.8.0) using the same WGS bam.file and co…
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The following options (available in `mmseqs search` but not in `mmseqs prefilter`) would be extremely useful when running a prefilter analysis:
```
-e evalue cut-off
--max-accept …
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The tests take ~40 minutes via Travis, which is running through all of the notebooks. Once we hit 50 minutes, Travis will abort the tests. Most of the cells run instantly, or with little delay, but so…