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I'd like to use adaptive banded global alignment (with affine gaps) instead of edlib. Switching between the different algorithms should be possible.
The best target for this is @ocxtal's https://gi…
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Hi there,
Excited to try this assembler with my HiFi reads, but I'm having trouble installing. Hoping someone can help me understand the following errors. I had no problem up until the `sh install.sh…
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[Class `ProteinEmbedding`](https://github.com/scikit-bio/scikit-bio/blob/545c9859635a5b8514bd9fd599475717c533f108/skbio/embedding/_protein.py#L29-L121) implements a data structure for the storage of p…
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Hi there! I'm attempting to perform a homology search for a single gene (a bacterial protein) across all sequenced bacterial genomes to estimate the % of species that carry the gene. Is there a way to…
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Hi,
```
import skbio
skbio.__version__
'0.5.5'
```
The example code here uses an aligner with the following scoring scheme:
Match:2, Mismatch:-1, all_gaps_penalties=1
```
from skbio im…
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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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这是一个文摘,梳理一下知识图谱的一些相关概念,semantical network, semantic web, linked data, knowledge graph。
一、 Semantic Network
```
semantic network = node + relation
```
语义网络不是什么新概念,其本质就是通过符号系统描述事物的关联。按照人们对事…
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Hi Quentin @qmarcou,
I am a new bioinformatics postdoc in Prof. Frederick Alt's lab. I have read your 2018 Nature Communication paper introducing the fantastic tool IGoR, and I am now trying to app…
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Hi, I have a set of 100,000 analyses (batched into 1000 jobs of 100 analyses each) which include running a diamond search. The searches involved are small (10-15 protein queries against a single prote…
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## Summary
This is a continuation of a discussion on the Slack channel with @tooky @brasmusson @mattwynne and others.
I've tried to cover as much background as I can given the limitati…