Python scripts for biologists
This project is currently suspended due to the fact that I found web is a more acceptable platform for the purpose. To this end, I am moving to a new project built on JavaScript, HTML, and CSS. Please follow the link below to learn more.
---> BiologyMeetWeb
This is a project for personal use at the very begining. It is not a program covering every piece of biology. The main purpose is just to make my routine work a bit easier and more streamlined. If you are looking for a advanced python scripts suit for biology, please give BioPython a shot.
The main functionalities of the scripts are listed below:
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process and analyze DNA or protein sequences - remove '\n','\t', '\r' and numbers that are in the DNA or protein sequences - get reversed complementory sequence - read a local fasta file - read a fastq file and plot quality scores - design primers - slice the sequence to pieces of length of interest - translate DNA or mRNA sequence to protein - find recognition sites of restriction enzymes - look up genetic codons - ...
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Search NCBI for the information about a gene, such as mRNA variants, mRNA sequences, CDS
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Search Uniprot for the information about a protein, such as AA sequence
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find and apply popular online tools in one place, such as PSIPRED
Please find Mybiotools demo.ipynb to explore how it works.
You are welcome to throw any comments or suggestion here. OR contact me @Mingzhang_Yang
At last, please feel free to fork it for your personalized use.