Roslin Bioinformatics - Haplofinder
Haplofinder is a simple python script designed to simplify identification of possible haplotype pairs when presented with an ambiguous sequence trace derived from a diploid organism. The context in which it was developed is the investigation of immune function in cattle, specifically the development of a sequence-based typing system for exon 2 of the BoLA-DRB3 gene. This exon has 94 known characterised alleles. The system takes an input file of known alleles and combines them in pairwise fashion to generate ambiguous traces. The ambiguous traces generated by sequencing are then compared directly against the pre-calculated pairs to identify possible matches. The script is not sophisticated, but works to fulfil the required function well.
It is provided here under the GNU public license in the hope that it will be useful. Should you wish to modify it, please feel free to do so (under the terms of the GPL), but also feel free to discuss ways in which the script might be modified with by contacting us directly so that your changes might benefit a wider audience.
Haplofinder can be downloaded by clicking on the link below