3
votes
1answer
39 views

How can I re-format my DNA motifs' position weight matrices?

I am working with a set of DNA motifs that are predicted as potential regulatory motifs (e.g. transcription factor binding sites). The motifs belong to several species, and I wanted to cluster these ...
5
votes
3answers
150 views

How easy is it to carry out de novo sequence assembly?

Today a colleague of mine asked the following question: " Assuming I need to build from 0, a chromosome of a fish, with short reads but no other reference whatsoever [de novo assembly]: ...
3
votes
1answer
91 views

Superposing DNA

I have a series of protein models with DNA docked. I now want to superpose the DNA on a reference DNA molecule and extract the translational distance applied and the rotation angle used. I can ...