Biopython
seq
| Biopython | seq | |
|---|---|---|
| 31 | 15 | |
| 4,171 | 634 | |
| 1.1% | - | |
| 9.6 | 0.7 | |
| 1 day ago | over 1 year ago | |
| Python | C++ | |
| GNU General Public License v3.0 or later | Apache License 2.0 |
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Biopython
- Invitación a proyecto - Biopython en Español
- Biopython – Python Tools for Computational Molecular Biology
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comparing the similarity between a set of protein sequences
Usearch will do all-against-all comparisons, cluster sequences, and produce alignments for each cluster. You can set the clustering threshold (proportion of residues identical). The alignments are in fasta format, which is pretty standard. If all you want is basic similarity it might be easiest to just write something that calculates normalized Hamming distances (typically called p-distances in the molecular evolution literature) between pairs of sequences. I suspect the biopython fasta reader (you can install biopython from https://biopython.org/) will be good enough.
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u/Responsible-Gas3852 comments on "Why is Cancer so Hard to Cure?"
Yes, the computing tool for biological computation.
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My boss is considering letting me take a programming course if I have some good reasons why.
Beside that their core lectures to non-computer scientists are public (survey), workshops by software carpentry move around the globe. Maybe your intent to seed hands-on knowledge is in similar tune before heading for biopython, bioperl, bioawk. It doesn't hurt to tap into resources initially written for non-labrats either, e.g. about regular expressions by programming historian.
- Can you run ScanProsite locally?
- How to iterate over the whole GRCh38 genome with python?
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Help they’re turning me into a programmer
Well, what language do you want to learn? What is your background so far? Assuming it is more on the side of biology, software carpentry's Python may eventually lead to biopython? Though there equally is a chance for AWK (Hack the planet's text! and bioawk...
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Biology related exercices and "challenges" to train by myself
I think you mind find something of a community around BioPython, which might be helpful. Just looking at the capabilities will probably be instructive as well.
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Joining the Open Source Development Course
Python is the main programming language I use nowadays. In particular numpy and pandas are of course extremely useful. I also use biopython package - a collection of software tools for biological computation written in Python by an international group of researchers and developers.
seq
- Bioinformatics programming language
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A Python-based programming language for high-performance computational genomics
> Seq is a Python-compatible language, and the vast majority of Python programs should work without any modifications
https://github.com/seq-lang/seq
- Seq – A programming language for computational genomics and bioinformatics
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Hacker News top posts: Sep 15, 2021
Seq: A programming language for high-performance computational genomics\ (17 comments)
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Seq: A programming language for high-performance computational genomics
They support both, and will deprecate Python 2 style soon.
https://github.com/seq-lang/seq/issues/223
What are some alternatives?
RDKit - The official sources for the RDKit library
Nim - Nim is a statically typed compiled systems programming language. It combines successful concepts from mature languages like Python, Ada and Modula. Its design focuses on efficiency, expressiveness, and elegance (in that order of priority).
biotite - A comprehensive library for computational molecular biology
adam - ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
bioconda-recipes - Conda recipes for the bioconda channel.
edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
Numba - NumPy aware dynamic Python compiler using LLVM
wyng-backup - Fast Time Machine-like backups for logical volumes & disk images
Pandas - Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
bowtie2 - A fast and sensitive gapped read aligner
PyDy - Multibody dynamics tool kit.
seq-genomics - Coursera Bioinformatics / Stepik Genome Sequencing with seq-lang