Editing Gene prediction (section)

===Other signals===
Among the derived signals used for prediction are statistics resulting from the sub-sequence statistics like [[k-mer]] statistics, [[Isochore (genetics)]] or [[Compositional domain]] GC composition/uniformity/entropy, sequence and frame length, Intron/Exon/Donor/Acceptor/Promoter and [[Ribosomal binding site]] vocabulary, [[Fractal dimension]], [[Fourier transform]] of a pseudo-number-coded DNA, [[Z-curve]] parameters and certain run features.<ref name="Saeys2007">{{cite journal | vauthors = Saeys Y, Rouzé P, Van de Peer Y | title = In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists | journal = Bioinformatics | volume = 23 | issue = 4 | pages = 414–20 | date = February 2007 | pmid = 17204465 | doi = 10.1093/bioinformatics/btl639 | doi-access = free }}</ref>

It has been suggested that signals other than those directly detectable in sequences may improve gene prediction. For example, the role of [[secondary structure]] in the identification of regulatory motifs has been reported.<ref name="Hiller2006">{{cite journal | vauthors = Hiller M, Pudimat R, Busch A, Backofen R | title = Using RNA secondary structures to guide sequence motif finding towards single-stranded regions | journal = Nucleic Acids Research | volume = 34 | issue = 17 | pages = e117 | year = 2006 | pmid = 16987907 | pmc = 1903381 | doi = 10.1093/nar/gkl544 }}</ref> In addition, it has been suggested that RNA secondary structure prediction helps splice site prediction.<ref name="Patterson2002">{{cite journal | vauthors = Patterson DJ, Yasuhara K, Ruzzo WL | title = Pre-mRNA secondary structure prediction aids splice site prediction | journal = Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | pages = 223–34 | year = 2002 | pmid = 11928478 }}</ref><ref name="Marashi2006a">{{cite journal | vauthors = Marashi SA, Goodarzi H, Sadeghi M, Eslahchi C, Pezeshk H | title = Importance of RNA secondary structure information for yeast donor and acceptor splice site predictions by neural networks | journal = Computational Biology and Chemistry | volume = 30 | issue = 1 | pages = 50–7 | date = February 2006 | pmid = 16386465 | doi = 10.1016/j.compbiolchem.2005.10.009 }}</ref><ref name="Marashi2006b">{{cite journal | vauthors = Marashi SA, Eslahchi C, Pezeshk H, Sadeghi M | title = Impact of RNA structure on the prediction of donor and acceptor splice sites | journal = BMC Bioinformatics | volume = 7 | pages = 297 | date = June 2006 | pmid = 16772025 | pmc = 1526458 | doi = 10.1186/1471-2105-7-297 | doi-access = free }}</ref><ref name="Rogic2006">{{Cite thesis |degree=PhD |title=The role of pre-mRNA secondary structure in gene splicing in ''Saccharomyces cerevisiae'' |url=http://www.cs.ubc.ca/grads/resources/thesis/Nov06/Rogic_Sanja.pdf |author=Rogic, S |year=2006 |publisher=University of British Columbia |access-date=2007-04-01 |archive-date=2009-05-30 |archive-url=https://web.archive.org/web/20090530023145/http://www.cs.ubc.ca/grads/resources/thesis/Nov06/Rogic_Sanja.pdf |url-status=dead }}</ref>