Editing Gene prediction (section)

== Pseudogene prediction ==

[[Pseudogenes]] are close relatives of genes, sharing very high sequence homology, but being unable to code for the same [[protein]] product. Whilst once relegated as byproducts of [[DNA sequencing|gene sequencing]], increasingly, as regulatory roles are being uncovered, they are becoming predictive targets in their own right.<ref name="Alexander2010">{{cite journal | vauthors = Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB | title = Annotating non-coding regions of the genome | journal = Nature Reviews. Genetics | volume = 11 | issue = 8 | pages = 559–71 | date = August 2010 | pmid = 20628352 | doi = 10.1038/nrg2814 | s2cid = 6617359 }}</ref> Pseudogene prediction utilises existing sequence similarity and ab initio methods, whilst adding additional filtering and methods of identifying pseudogene characteristics.

Sequence similarity methods can be customised for pseudogene prediction using additional filtering to find candidate pseudogenes. This could use disablement detection, which looks for nonsense or frameshift mutations that would truncate or collapse an otherwise functional coding sequence.<ref name="Svensson2006">{{cite journal | vauthors = Svensson O, Arvestad L, Lagergren J | title = Genome-wide survey for biologically functional pseudogenes | journal = PLOS Computational Biology | volume = 2 | issue = 5 | pages = e46 | date = May 2006 | pmid = 16680195 | pmc = 1456316 | doi = 10.1371/journal.pcbi.0020046 | bibcode = 2006PLSCB...2...46S | doi-access = free }}</ref> Additionally, translating DNA into proteins sequences can be more effective than just straight DNA homology.<ref name="Alexander2010" />

Content sensors can be filtered according to the differences in statistical properties between pseudogenes and genes, such as a reduced count of CpG islands in pseudogenes, or the differences in G-C content between pseudogenes and their neighbours. Signal sensors also can be honed to pseudogenes, looking for the absence of introns or polyadenine tails.
<ref name="Zhang2004">{{cite journal | vauthors = Zhang Z, Gerstein M | title = Large-scale analysis of pseudogenes in the human genome | journal = Current Opinion in Genetics & Development | volume = 14 | issue = 4 | pages = 328–35 | date = August 2004 | pmid = 15261647 | doi = 10.1016/j.gde.2004.06.003 }}</ref>