http://precedings.nature.com/users/f3ae9e85aba7fb7172c3d102af881710/ Documents posted by Natarajan Ganesan Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/2909/version/1 We have analyzed the linkers in group-I introns, a characteristic region that is crucial to the folding and splicing process of the folded RNA, in seventy sequences spreading across r-RNA, t-RNA and organelle genes from various organisms including algae, fungi and protozoa. The study revealed a high degree of consensus of specific adenine residues in J3/4, J6/7 and J8/7 stems of the linker regions that were required to stabilize the local orientation, either as single residue or by forming unusual base pairs along with divalent metal ions. Conservation of these residues in the Group-I intron linkers suggests their significant contribution to the folded structure whose bonding and geometry recruit metal ions to interact in stabilizing the folded nature of RNA. http://precedings.nature.com/documents/2909/version/1 Tue, 03 Mar 2009 16:24:11 UTC Phylogeny of conserved adenines in linkers of Group-I introns hdl:10101/npre.2009.2909.1 2009-03-03 Natarajan Ganesan Nature Precedings 2009-03-03T16:24:11Z Manuscript Molecular Cell Biology Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/2492/version/1 Background: No approaches have yet been developed to allow instant searching of the World-Wide-Web by just entering a string of sequence data. Though general search engines can be tuned to accept ‘processed’ queries, the burden of preparing such ‘search strings’ simply defeats the purpose of quickly locating highly relevant information. Unlike ‘sequence similarity’ searches that employ dedicated algorithms (like BLAST) to compare an input sequence from defined databases, a direct ‘sequence based’ search simply locates quick and relevant information about a blunt piece of nucleotide or peptide sequence. This approach is particularly invaluable to all biomedical researchers who would often like to enter a sequence and quickly locate any pertinent information before proceeding to carry out detailed sequence alignment. Results: Here, we describe the theory and implementation of a web-based front-end for a search engine, like Google, which accepts sequence fragments and interactively retrieves a collection of highly relevant links and documents, in real-time. e.g. flat files like patent records, privately hosted sequence documents and regular databases. Conclusions: The importance of this simple yet highly relevant tool will be evident when with a little bit of tweaking, the tool can be engineered to carry out searches on all kinds of hosted documents in the World-Wide-Web.Availability: Instaseq is free web based service that can be accessed by visiting the following hyperlink on the WWWhttp://instaseq.georgetown.edu http://precedings.nature.com/documents/2492/version/1 Tue, 11 Nov 2008 20:14:41 UTC Searching the World-Wide-Web using nucleotide and peptide sequences hdl:10101/npre.2008.2492.1 2008-11-11 Natarajan Ganesan Nature Precedings 2008-11-11T20:14:41Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/