GSoC-2021-Bioinformatics-Notebooks-for-WormBase

This repository comprises of tutorials to help you get familiarised with the data on WormBase sites. The tutorials are in the form of Jupyter-Notebooks which will walk you through various methods for data retrieval and several types of basic bioinformatics analyses on this data. You can easily access all the tutorials here and run them using mybinder:

Table of Contents:

-Setup:

Data Retrieval

• Exploring WormBase FTP:
• WormMine using intermine:
• Getting data from ParaSite:
• Extracting Gene level information:

Analyses

• BLAST Alignment:
• BLAT Alignment:
• ePCR:
• Pairwise Sequence Alignment:
• Multiple Sequence Alignment:
• Ontology Analyses:
• Enrichment Analyses:
• Literature-based Analyses:

Simple data utilities

• Genome Data Viewer:
• WormCat: This is currently unavailable on Binder due to R-magic dependency. It will be resolved soon! IPython version
• Chromosome Map: