Probe mining with OligoArray

Probe Mining with OligoArray

 

The documentation and scripts provided in this section will assist users in using OligoArray to discover FISH probe sequences - either in the genomes we have already mined using different parameters or in genomes for which we have not yet run OligoArray. Please keep in mind that probe discovery is considerably more complex than working with the Oligopaints .bed files we have already generated, particularly in the amount of computational resources required. Probe discovery is greatly aided by an intermediate understanding of UNIX, familiarity with programming languages such as python, perl, and bash, and access to a computing cluster.

Guide to mining the Drosophila Hox clusters for probes with 50 bases of genomic homology:

Probe_mining_hox_example.pdf

Updated 8/27/12

Probe mining scripts:

probe_mining_scripts.tar.gz

/hox_example/ contents:

hox_example.tar.gz

Whole-genome sequence files for making custom BLAST databases:

ce6.fas.gz

dm3.fas.gz

tair10.fas.gz

mm9.fas.gz

hg19.fas.gz