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Dear Wayne,
Every now and then I'm looking for freely available molecular biology software, e.g. to give it to our beginner students or use it by myself.
For my own little problems I'm actually u…
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Description: I propose adding a new function molecular_weight() to the BioSequences package that calculates the average or monoisotopic molecular weight of a protein or nucleic acid sequence. The func…
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Hi all,
stumbled upon this paper describing the mapping of PDB residue id's to the ones in the sequence deposited in Uniprot:
- Choudhary, P.; Anyango, S.; Berrisford, J.; Varadi, M.; Tolchard, …
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Please read that and implement it in quality-control.py. Basically we should use trim_galore as the main tool for quality control. In this script the input is fastq files and outputs are validated fas…
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**Is your feature request related to a problem? Please describe.**
I think it's quite common that FLASH can't really merge the PE reads, For example:
- 1. amplicon sequence too long or too short…
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Hi there,
This is not so much an issue as it is a question. When I run Crass I end up with multiple .gv files for one group/array (if I have read the documentation correctly) - am I correct in thi…
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Could you please provide the following information:
1. example syntax for DNA_FT.py
2. example input and output file pair
3. list of dependencies for installation (preferably using downloads all …
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Starting to think about this in the context of generating a lot of 10x VDJ data... it seems we will want to (eventually) have a way for `Clone`s to contain `cell`s (see https://github.com/airr-communi…
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## Background
`GenBank` format ("GenBank Flat File Format") is a genomic format that describes nucleotide sequences and their protein translations. `GenBank` file (`.genbank`, `.gb`, `.gbk`) is a s…
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Cloned git repo today clean Ubuntu (AWS c5a.4xlarge instance with Ubuntu 20.04).
Installed dendropy dependency.
```
cd example
python3 ../magus.py -d outputs -i unaligned_sequences.txt -o magus_…