benlangmead / comp-genomics-class Goto Github PK

There appears to be a broken link in notebooks/FASTA.ipynb.

@BenLangmead First a big thank you for all these excellent resources. They are both world-class and unique in their clarity and quality.

The license of the code here is overall GPL per https://github.com/BenLangmead/comp-genomics-class/blob/master/LICENSE

I was wondering if you would consider something else that I could reuse with Apache-licensed code in particular the code for the suffix tree, suffix array and FM index in https://github.com/BenLangmead/comp-genomics-class/blob/master/notebooks/fm.py ,
https://github.com/BenLangmead/comp-genomics-class/blob/master/notebooks/sa.py and https://github.com/BenLangmead/comp-genomics-class/blob/master/notebooks/suf_tree.py

It could be an LGPL, a GPL with exception, Apache, BSD, MIT or anything that could mesh well with Apache-licensed code.

Thank you very much for your kind consideration!

Hi Dr. Langmead,

The notebook for the naive exact string matching algorithm doesn't seem to be there in the repository. Probably you missed to add it.

Thank you very much for the great tutorial on BW and FM! This is a great read. I think this is a type on Page 10, section 4, the third last line.
rankAll[c][i0] − x gives the same value we would have found in rankAll[c][i] − x.
I think the latter -x should be removed.

hi ben, I am a new student about this field. I wonder do there have online videos about computational genomics class?

thank you !

I was going through FASTA.ipynb and had troubles downloading FASTA reference. Backtracking URL I have found a README (link below, because MD rendering doesn't allow ftp URLs) and it says all content is moved elsewhere.

ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/README.txt