Changes

==Finding pseudogenes==

==Finding pseudogenes==

Pseudogenes are often difficult to parse from the large amount of non-coding base pairs in the genome. Convention requires two elements to be present to label a sequence a pseudogene. The first is [[homology]] which is the requirement that a sequence be demonstrated to descend from a functional copy of the gene and the second is non-functionality which is the requirement that the gene not code for a protein in the organism in question. <ref name=sciam />

Pseudogenes are often difficult to parse from the large amount of non-coding base pairs in the genome. Convention requires two elements to be present to label a sequence a pseudogene. The first is [[homology]] which is the requirement that a sequence be demonstrated to descend from a functional copy of the gene and the second is non-functionality which is the requirement that the gene not code for a protein in the organism in question. <ref name=sciam />

 

Since all pseudogenes are descended from a functioning gene the first step is to find the parent gene that it descended from. This is done by using computer programs to compare sequences of DNA across species. <ref name=sciam /> This is a large computational problem but by keeping in mind the phylogenetic relationships between species the search time can be decreased by looking at species that share a more recent common ancestor.<ref name=mito>Bensasson, D., Zhang, D., Hartl, D., Hewitt, G. (2001). Mitochondrial pseudogense: evolution's misplaced witness. Trends in Ecology and Evolution 16: 314-321. [http://www.ioz.ac.cn/department/agripest/group/zhangdx/ZDX-s-pdf%5CTREE2001-Updated_numt.PDF]</ref>  Once a functioning copy of a gene is detected its sequence is compared to the pseudogene. A high correlation in base pairs is used to assign homology. Non-functionality can be demonstrated by attempting to transcribe the sequence in-vitro. <ref name=sciam />  

==Pseudogenes and neutral selection theory==

==Pseudogenes and neutral selection theory==