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12x coverage 454/Sanger Hybrid Assembly of Cucumber (Cucumis sativus L. cv.Borszczagovski) genome - the most efficient way to begin post genomic era Nature Precedings
Rafał Wóycicki; Justyna Witkowicz; Magdalena Pawełkowicz; Ewa Siedlecka; Wojciech Gutman; Wojciech Pląder; Anna Seroczyńska; Mieczysław Śmiech; Katarzyna Niemirowicz-Szczytt; Stanisław Karpiński; Stefan Malepszy; Zbigniew Przybecki.
New sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects. 
We present here approaches undertaken on the way to the draft assembly the cucumber (Cucumis sativus L. cv. Borszczagowski) genome done with the use of 8x unpaired and 4x paired (3 Kbp) pyrosequenced 454 XLR Titanium reads, together BAC library ends fragments (12,7x physical coverage). Two different assembly approaches, namely Celera and Celera/Arachne were finally used. The Celera result was 15’196 contigs of 197 Mbp length and N50 27’086 bp and 4’157 scaffolds of 224 Mbp length...
Tipo: Poster Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5466/version/1
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BRAGOMAP - a new Perl script for high throughoutput blast results analysis including GO and MapMan automatic annotations Nature Precedings
Rafal Woycicki; Wojciech Gutman; Zbigniew Przybecki.
Analyzing of sequences similarities is the first and most important method used to find out the function of unknown nucleotides. Searching of homologs should be done carefully not to loose any important ones. Having thousands of results from various long-read sequencing projects (ie. differentially expressed tags, genomic polymorphons or BAC ends), the by-hand ability to retrieve interesting (to our goal) similarities in hundreds of Blast results decreases rapidly. Decreasing the number of retrieved sequences by giving more stringency in e-value threshold or displaying less results could lead to false deductions. Functional genomics, proteomics and metabolomics could give us answers to the role of nucleotide sequences. It makes the need to annotate as much...
Tipo: Poster Palavras-chave: Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3900/version/1
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