Biopython
Official git repository for Biopython (originally converted from CVS) (by biopython)
orfipy
Fast and flexible ORF finder (by urmi-21)
| Biopython | orfipy | |
|---|---|---|
| 31 | 2 | |
| 4,171 | 46 | |
| 1.1% | - | |
| 9.6 | 1.8 | |
| 1 day ago | over 2 years ago | |
| Python | Python | |
| GNU General Public License v3.0 or later | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Biopython
Posts with mentions or reviews of Biopython.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-05-12.
- 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.
orfipy
Posts with mentions or reviews of orfipy.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-08-08.
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Looking for a tool to convert a whole fasta file with CDS sequences to a fasta file with protein sequences.
You can probably use or adapt https://github.com/urmi-21/orfipy. I've never used this but it looks fantastic.
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Question about ORF finder
You don't need any specific hardware to run most bioinformatics programs. There is a web application of ORF finder and if you want to run large amounts of analyses you probably want to run them in a Linux environment. Look at Windows Subsystem for Linux if you are a Windows user. You may also be interested in new ORF finders like this one: https://github.com/urmi-21/orfipy
What are some alternatives?
When comparing Biopython and orfipy you can also consider the following projects:
RDKit - The official sources for the RDKit library
galaxy - Data intensive science for everyone.
biotite - A comprehensive library for computational molecular biology
pyrodigal - Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
bioconda-recipes - Conda recipes for the bioconda channel.
reCOGnizer - A tool for domain based annotation with databases from the Conserved Domains Database
Numba - NumPy aware dynamic Python compiler using LLVM
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
PyDy - Multibody dynamics tool kit.
weblogo - WebLogo 3: Sequence Logos redrawn
statsmodels - Statsmodels: statistical modeling and econometrics in Python
bccb - Incubator for useful bioinformatics code, primarily in Python and R