By Laura Poliseno
Providing an inventory of equipment priceless either to those that desire to examine pseudogenes and to those that truly are looking to keep away from their inadvertent detection, Pseudogenes: features and Protocols explores recommendations related to pseudogenic DNA, RNA, and peptides/proteins, as soon as believed to lack any performance, yet referred to now to be fascinated by advanced regulatory circuits. After a number of introductory chapters that evaluation the services up to now attributed to pseudogenes, this thorough quantity delves into equipment for pseudogene identity, for the detection of pseudogene transcription and translation, and for the research of the features of pseudogenic RNA and proteins, in addition to tips on how to steer clear of pseudogene detection whilst the point of interest of the study is their hugely homologous parental opposite numbers. As a part of the hugely winning Methods in Molecular Biology sequence, chapters function the type of certain descriptions and implementation suggestion that guarantees winning leads to the lab.
Authoritative and sensible, Pseudogenes: features and Protocols will give a contribution to the excessive curiosity of the medical group towards pseudogenes, whereas stimulating the notion of pseudogene - founded study tasks and offering experimental protocols which may facilitate their execution.
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Additional resources for Pseudogenes : functions and protocols
The amplitudes of Fourier harmonics (or structure factors) are expressed as Fαα (qn ) = ρα (qn ) ρα* (qn ) , (2) where the asterisk denotes complex conjugation. The zeroth harmonics, depending only on the nucleotide composition, do not contain structural information and will be discarded below. The structure factors will always be normalized with respect to the mean spectral values, which are determined by the exact sum rules, f αα (qn ) = Fαα (qn ) / Fαα ; Fαα = N α ( M − N α ) / M ( M − 1) , (3) where Nα is the total number of nucleotides of type α in a sequence of length M.
Org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res 35:D55–D60 2. Zhang Z, Harrison PM, Liu Y et al (2003) Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in human genome. Genome Res 13: 2541–2558 3. Balakirev E, Ayala FJ (2003) Pseudogenes: are they “junk” or functional DNA? Annu Rev Genet 37:123–151 4. Pink RC, Wicks K, Caley DP et al (2011) Pseudogenes: pseudo-functional or key regulators in health and disease.
Annotation of pseudogenes using sequence homology has also been applied to fungi, specifically yeasts. In budding yeast, which has few spliced genes, pseudogenes were annotated either though detection of “disabled open reading frames” (dORFs) or “mergeable open reading frames” (mORFs) in the genomic DNA . dORFs were the largest “ORFs” arising from a fragment of disabled protein-sequence homology that had been detected in the genomic DNA using the FASTA suite . mORFs were pairs of ORFs that Using Sequence Homology to Find Pseudogenes 33 could be merged into one longer ORF with a mid-sequence stop codon.
Pseudogenes : functions and protocols by Laura Poliseno