A (quite messy but usable) Perl program to infer gene and its subfeatures on a (longer, not sure with shorter) suspected corresponding gene sequence in a new, but almost identical genome. Uses NCBI BLAST+ whenever possible.
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This is a program to map variances that were retrieved on a created, mostly similar genome, to the origin/base genome. Takes in variances (SNPs and INDELs only for now) in VCF format, gets its nearby X sequences to the left and right and these are BLAST-ed into the original genome. Best hit is selcted and the sequence is reduced again to to infer the location in new genome.
VCF TO GFF3 Converter | Sharing this since I haven't found one that works for me. This one (https://gist.github.com/danwiththeplan/3989411) didn't. I think there's one for iplant but it's not public.
A set of files for HTTP Basic logout mechanism. Specifically designed for the internal project I am working on with my company but you can easily customize it to suit your needs.
A set of (meant to be interactive) shell scripts (and maybe in the future, C or other programs), to backup files in the server root directory and database dumps, related to the operation of the trio Drupal-Chado-Tripal as seen in http://gmod.org/wiki/Tripal_Tutorial_(v1.0)