Editing Baum–Welch algorithm (section)

====Finding genes====

=====Prokaryotic=====
The [[GLIMMER]] (Gene Locator and Interpolated Markov ModelER) software was an early [[locus (genetics)|gene-finding]] program used for the identification of coding regions in [[prokaryotic]] DNA.<ref name="GLIMMER paper">{{cite journal |last1=Salzberg |first1=Steven |first2=Arthur L. |last2=Delcher |first3=Simon |last3=Kasif |first4=Owen |last4=White |title=Microbial gene identification using interpolated Markov Models |journal=Nucleic Acids Research |year=1998 |volume=26 |issue=2 |pages=544–548 |doi=10.1093/nar/26.2.544 |pmid=9421513 |pmc=147303 }}</ref><ref name="GLIMMER web">{{cite web |title=Glimmer: Microbial Gene-Finding System |url=http://ccb.jhu.edu/software/glimmer/index.shtml |publisher=Johns Hopkins University - Center for Computational Biology }}</ref> GLIMMER uses Interpolated Markov Models (IMMs) to identify the [[exon|coding regions]] and distinguish them from the [[introns|noncoding DNA]]. The latest release (GLIMMER3) has been shown to have increased [[specificity (statistics)|specificity]] and accuracy compared with its predecessors with regard to predicting translation initiation sites, demonstrating an average 99% accuracy in locating 3' locations compared to confirmed genes in prokaryotes.<ref>{{cite journal |last1=Delcher |first1=Arthur |first2=Kirsten A. |last2=Bratke |first3=Edwin C. |last3=Powers |first4=Steven L. |last4=Salzberg |title=Identifying bacterial genes and endosymbiont DNA with Glimmer |journal=Bioinformatics |year=2007 |volume=23 |issue=6 |pages=673–679 |doi=10.1093/bioinformatics/btm009 |pmid=17237039 |pmc=2387122 }}</ref>

=====Eukaryotic=====
The [[GENSCAN]] webserver is a gene locator capable of analyzing [[eukaryotic]] sequences up to one million [[base-pairs]] (1 Mbp) long.<ref>{{cite web |last=Burge |first=Christopher |title=The GENSCAN Web Server at MIT |url=http://genes.mit.edu/GENSCAN.html |access-date=2 October 2013 |archive-url=https://web.archive.org/web/20130906115338/http://genes.mit.edu/GENSCAN.html |archive-date=6 September 2013 |url-status=dead }}</ref> GENSCAN utilizes a general inhomogeneous, three periodic, fifth order Markov model of DNA coding regions. Additionally, this model accounts for differences in gene density and structure (such as intron lengths) that occur in different [[Isochore (genetics)|isochores]]. While most integrated gene-finding software (at the time of GENSCANs release) assumed input sequences contained exactly one gene, GENSCAN solves a general case where partial, complete, or multiple genes (or even no gene at all) is present.<ref>{{cite journal |last1=Burge |first1=Chris |first2=Samuel |last2=Karlin |title=Prediction of Complete Gene Structures in Human Genomic DNA |journal=Journal of Molecular Biology |year=1997 |volume=268 |pages=78–94 |doi=10.1006/jmbi.1997.0951 |pmid=9149143 |issue=1 |citeseerx=10.1.1.115.3107 }}</ref> GENSCAN was shown to exactly predict exon location with 90% accuracy with 80% specificity compared to an annotated database.<ref>{{cite journal |last1=Burge |first1=Christopher |first2=Samuel |last2=Karlin |title=Finding the Genes in Genomic DNA |journal=Current Opinion in Structural Biology |year=1998 |volume=8 |issue=3 |pages=346–354 |doi=10.1016/s0959-440x(98)80069-9 |pmid=9666331 |doi-access=free }}</ref>