we are building a parallel-computing tool capable of processing a) virus-genome vs b) human-genome or animal genome. Searching for subsequences from a) along b)
the Question is: how long would be the virus subsequence and wich region of the human or animal genome/chromosomes should we look?
A lot of these questions will depend on how long ago the retrovirus entered the genome (if it's becoming endogenised within the genome, fragments will decay in length over time). I recommend you read some of Aris Katzourakis's papers about endogenous viruses (incl retroviruses) eg http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004332 and more here https://scholar.google.co.uk/citations?user=slSa2ecAAAAJ
these databases would help
https://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/
http://herv.img.cas.cz
http://variation.osu.edu/rtcgd/
Tanks for advice. There is a first result for the search process, you may take a look here.
https://www.researchgate.net/project/Searching-For-Virus-along-Human-Animal-Reference-Genome
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