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https://github.com/fomightez/length_binder

Use Jupyter environment to look at protein length for various organisms. Active form served via Binder system.
https://github.com/fomightez/length_binder

Last synced: 21 days ago
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Use Jupyter environment to look at protein length for various organisms. Active form served via Binder system.

Host: GitHub
URL: https://github.com/fomightez/length_binder
Owner: fomightez
License: mit
Created: 2018-06-26T19:22:53.000Z (over 6 years ago)
Default Branch: master
Last Pushed: 2018-06-27T14:38:13.000Z (over 6 years ago)
Last Synced: 2024-11-07T14:13:14.203Z (2 months ago)
Language: Jupyter Notebook
Homepage:
Size: 18.1 MB
Stars: 1
Watchers: 2
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

Awesome Lists containing this project

README

        [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/fomightez/length_binder/master?filepath=index.ipynb)

# length_binder

Use Jupyter environment to look at protein length for various organisms. Served via Binder system.  

In response to a suggested query [here](https://twitter.com/PlantEvolution/status/1011423582512144385).

Click the `launch binder` badge anywhere on this page to launch the active Jupyter environment.

[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/fomightez/length_binder/master?filepath=index.ipynb)

Data sources

------------

The sources for protein length data:

- *Saccharomyces cerevisiae* S288C (yeast) - At the time of running the code it is interactively collected from YeastMine using Intermine's webservice to retrieve length of all proteins, which is based on [this template](https://yeastmine.yeastgenome.org/yeastmine/template.do?name=Organism_Protein&scope=all).

![Intermine](https://github.com/intermine/design-materials/blob/master/logos/intermine/intermine-300x37.png?raw=true)

- *Arabidopsis thaliana* (thale cress) - the repo includes a file obtained June 2018 from [Genome Annotation at TAIR](https://www.arabidopsis.org/portals/genAnnotation/gene_structural_annotation/annotation_data.jsp). Specifically, if you follow the link for [the TAIR ftp site](ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR9_genome_release/) from the text under 'Data availability', it leads to page that features [TAIR9_sequences](ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR9_genome_release/) among the list that you can click on to get to a page where you can download [TAIR9_pep_20090619](ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR9_genome_release/TAIR9_sequences/TAIR9_pep_20090619).

- *Drosophila melanogaster* (fruit fly) - the repo includes a file obtained June 2018 from [Proteomes - Drosophila melanogaster (Fruit fly)](https://www.uniprot.org/proteomes/UP000000803) by clicking on the 'Download' tab under `Components` in middle of the page.