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LaTcOm: a web server for visualizing rare codon clusters in coding sequences.

TitleLaTcOm: a web server for visualizing rare codon clusters in coding sequences.
Publication TypeJournal Article
Year of Publication2011
AuthorsTheodosiou, Athina, and V. J. Promponas
JournalBioinformatics (Oxford, England)
Date Published2011 Dec 22
ISSN1367-4811
KeywordsBioinformatics, Computational Biology, Computational Genomics, Protein Structure, RNA, Sequence Analysis
Abstract

SUMMARY: 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. AVAILABILITY: LaTcOm is freely available online at the URL http://troodos.biol.ucy.ac.cy/latcom.html. CONTACT: vprobon@ucy.ac.cy SUPPLEMENTARY INFORMATION: Available at Bioinformatics online.

URLhttp://bioinformatics.oxfordjournals.org/cgi/content/abstract/btr706? ijkey=R4Lh1MSCSCovIRe&keytype=ref
DOI10.1093/bioinformatics/btr706


by Dr. Radut.