http://precedings.nature.com/tags/nucleotide Recently posted documents tagged with 'nucleotide' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3593/version/2 Oil palm is the second largest source of edible oil, which meets one-fifth of global demands of oils and fats. Expressed sequence tag (EST) sequencing programs have provided a wealth of information, identifying novel genes from a broad range of organisms and providing an indication of gene expression level in particular tissues. It also provides the richest source of biologically useful SNPs due to the relatively high redundancy of gene sequence, the diversity of genotypes represented within databases. EST based SNPs are potential molecular markers and aid in genetic improvement. A total of 21062 and 2053 polymorphic (SNP and Indel) sites in E. guineensis species and in E. oleifera, 4955 SNPs and 1172 Indels were detected. SNP(17.5/kbp) and Indel(4.1/kbp) frequency was higher in E. oleifera than E. guineensis species (16.8/kbp, 1.6/kbp). E. oleifera showed higher transition to transversion ratio (1.40) than in E. guineensis (1.02). The ratio of Ts vs Tv showed, the genetic divergence is occurring in this crops in different fashion and E. guineensis had diverged more than E. oleifera. We provide the results of the study as online database (http://riju.byethost31.com/oilpalm/) for use by oil palm breeders. http://precedings.nature.com/documents/3593/version/2 Thu, 24 Sep 2009 09:03:36 UTC Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm Elaeis guineensis and E. oleifera hdl:10101/npre.2009.3593.2 2009-09-24 Aikkal Riju Nature Precedings 2009-09-24T09:03:36Z Manuscript Genetics & Genomics Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3593/version/1 Oil palm is the second largest source of edible oil, which meets one-fifth of global demands of oils and fats. Expressed sequence tag (EST) sequencing programs have provided a wealth of information, identifying novel genes from a broad range of organisms and providing an indication of gene expression level in particular tissues. It also provides the richest source of biologically useful SNPs due to the relatively high redundancy of gene sequence, the diversity of genotypes represented within databases. EST based SNPs are potential molecular markers and aid in genetic improvement. A total of 21062 and 2053 polymorphic (SNP and Indel) sites in E. guineensis species and in E. oleifera, 4955 SNPs and 1172 Indels were detected. SNP(17.5/kbp) and Indel(4.1/kbp) frequency was higher in E. oleifera than E. guineensis species (16.8/kbp, 1.6/kbp). E. oleifera showed higher transition to transversion ratio (1.40) than in E. guineensis (1.02). The ratio of Ts vs Tv showed, the genetic divergence is occurring in this crops in different fashion and E. guineensis had diverged more than E. oleifera. We provide the results of the study as online database (http://riju.byethost31.com/oilpalm/) for use by oil palm breeders. http://precedings.nature.com/documents/3593/version/1 Wed, 12 Aug 2009 11:59:35 UTC Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm Elaeis guineensis and E. oleifera hdl:10101/npre.2009.3593.1 2009-08-12 Aikkal Riju Nature Precedings 2009-08-12T11:59:35Z Manuscript Genetics & Genomics 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/