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I used spaln to annotated a gene structure in de-nove assembly using a homologous protein, but spaln report error (Segmentation fault (core dumped)). The command as follow
spaln -Q3 -O0 -KP -C1 -M100…
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Hi @axelf4 I just found out about this project. I'm the guy who created `flex`. As far as I can see, hotfuzz is like `flex` but presumably better in every possible way. If that is true, I think we …
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I suggest using LCS to rank matches:
https://en.wikipedia.org/wiki/Longest_common_subsequence_problem#Solution_for_two_sequences
Matches with lower number of substrings would come before matches with…
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Hello, I'm getting a segfault when building the latest version: 817ba03fc19e0fb2076381eb9536ff99240bd468
Using this graphmap command line:
graphmap align --threads 1 --ref Chlamy_and_lambda.fa --…
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Hi, I'm a long time LateXTools Linux user, and now that I had to move to Windows I am trying to reproduce the same workflow I have on Linux.
The problem I have is that, whenever I try to compile on…
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Hello, the following algorithm is intended to use the Gotoh algorithm
aligner = PairwiseAligner() # for example
aligner.mode = 'global'
aligner.query_extend_gap_score = x
aligner.query_open_gap_…
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This is not for a bug - I'm trying to determine if biopython has a specific feature and can't find it on the docs/in the code. This probably means the feature does not exist, but thought I would ask.
…
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### Does this problem persist on the current master?
- [X] I have verified the issue on the current master
### Is there an existing issue for this?
- [X] I have searched the existing issues
### Cu…
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Here are some remarks I had while reading your paper. I'm bundling them in a single issue. Feel free to disagree with them though, and I may well be wrong myself once or twice; some others of these wi…
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If you call `align_it("", "some long sequence", ...)`, there is a memory leak in the C++ code. I worked around it in issue #409 by not calling the method when one of the strings is blank. However, it …