alby: Alignment-Based local homololgY

Given one query sequence and two or more subject sequences, we’d like to find the closest neighbor among the subjects as we move along the query. Our experimental program alfy for Alignment-Free local homologY, is one solution to this problem. The scripts collected here are meant as an alignment-based alternative.

Authors

Beatriz Vieira-Mourato & Bernhard Haubold

Dependencies

The programs in this repository depend on ncbi-blast+, bedtools, and the programs of the Biobox package. On a Debian-type system, these three dependencies can be installed by running

bash scripts/setup.sh

Now we can set up the directory tutorial and change into it.

make tutorial
cd tutorial

This contains the scripts to follow the tutorial.