title: LaTcOm: a web server for visualizing rare codon clusters in coding sequences.
abstract: We present LaTcOm, a new web tool, which offers several alternative methods for 'rare codon cluster' (RCC) identification from a single and simple graphical user interface. In the current version, three RCC detection schemes are implemented: the recently described %MinMax algorithm and a simplified sliding window approach, along with a novel modification of a linear-time algorithm for the detection of maximally scoring subsequences tailored to the RCC detection problem. Among a number of user tunable parameters, several codon-based scales relevant for RCC detection are available, including tRNA abundance values from Escherichia coli and several codon usage tables from a selection of genomes. Furthermore, useful scale transformations may be performed upon user request (e.g. linear, sigmoid). Users may choose to visualize RCC positions within the submitted sequences either with graphical representations or in textual form for further processing.
  
  
  BACKGROUND
  LaTcOm is freely available online at the URL http://troodos.biol.ucy.ac.cy/latcom.html.
authors.affiliation: Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, PO Box 20537, CY 1678, Nicosia, Cyprus.
authors.forename: Athina
authors.initials: A
authors.lastname: Theodosiou
authors.forename: Vasilis J
authors.initials: VJ
authors.lastname: Promponas
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D003062:Codon; D004926:Escherichia coli / Q000235:genetics; D020407:Internet; D012343:RNA, Transfer / Q000378:metabolism; D012984:Software
chemical_list: D003062:Codon; D012343:RNA, Transfer