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After testing out the striped smith-waterman algorithm on some largish datasets, I'm noticing a failure that is not expected. Below is a small test case replicating this issue (blosum matrix can be f…
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Shuji,
Thank you for contributing such valuable code!
After reading your code and the original paper "End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman", I have …
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Hi, when i try to run `./fetregister fet/5_0.05.fcb hv_c3_1_fine_to_coarse.conf -v`, then it always output segmentation fault such as
`Reading configuration file...
Done in 0.073 sec.
# Frames =…
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Affine alignment is not working, but simple edit distance works.
```
strucseq = "KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKG…
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i was hoping someone may be able to provide some more information on how to use these parameters, and what are reasonable values (mainly for `margin`) in different contexts. for example, several of th…
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Edlib does pairwise (1 vs 1) alignment, and while it can also be used for 1 vs N or N vs N that way, it would be interesting to see if implementing direct support for 1 vs N or N vs N in it could offe…
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## *Repository Creation Request*
Use this to get your experiment repository created or updated on GitHub under Virtual Labs organization.
1. #### Coordinating Institute: Amrita Vishwa Vidyapeetham…
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Hi,
I have a big genome with 46,139,523,234 bases and 20131 contigs.
Here is the summary of the longest contigs.
```
ptg000004l 169819904
ptg000441l 158822330
ptg000279l 109104046…
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Testing for #9, the good news is using the --compliant switch for PROKKA apparently allows the script to continue beyond where it would previously crash, but then clinker engages in slow, one-thread, …
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I ran into some issues with the pairwise alignment of sequences read from different files. Although the exact issue varies from case to case, it seems that the first alignment produces the correct res…