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ETC: Extender of Terminated ContigsExtender of Terminated Contigs
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Extender of Terminated Contigs
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ETC: Extender of Terminated Contigs | etc.opensequence.org Reviews
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Extender of Terminated Contigs
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Results - ETC: Extender of Terminated Contigs
http://etc.opensequence.org/figures/results
ETC: Extender of Terminated Contigs. First and second run). Ssake (default) TQS (modified, threshold 5). Ssake (default) PrimRemove (1 shift, 3 errors). Ssake (default) PrimRemove (1 shift, 3 errors) TQS (modified, threshold 5) (first removing reads with primer sequence than trimming). Reads resulting from PCR error, might still have resulted in termination. A path assembler should be able to resolve these branching points. To test this, ABySS was used. 5(old fig num) Figure 11:. For a path-assembler cap...
Paper - ETC: Extender of Terminated Contigs
http://etc.opensequence.org/paper
ETC: Extender of Terminated Contigs. Updated Sept 30, 2009. Short read assembly pipeline using scripted filters, de novo assembly and manual extension of terminated contigs. For the case study, the partial chloroplast genome. Homopolymer regions, a large inverted repeat, and low coverage. Is an organelle within the cells of photosynthetic organisms. Its function is to capture light energy eventually leading to the production of ATP (a unit of energy.) It is thought to have originated through endo...Stron...
Presentation - ETC: Extender of Terminated Contigs
http://etc.opensequence.org/paper/presentation
ETC: Extender of Terminated Contigs. These are the slides used during my Presentation on Aug 12th at the McNair Symposium.
Resources - ETC: Extender of Terminated Contigs
http://etc.opensequence.org/resources
ETC: Extender of Terminated Contigs. Only listing resources used for the project. AbySS http:/ www.bcgsc.ca/platform/bioinfo/software/abyss. Velvet http:/ www.ebi.ac.uk/ zerbino/velvet/. Edena http:/ www.genomic.ch/edena.php. Ssake http:/ www.bcgsc.ca/platform/bioinfo/software/ssake. QSRA http:/ qsra.cgrb.oregonstate.edu/. Sharcgs http:/ sharcgs.molgen.mpg.de/. SHORTY (designed for paired-read only) http:/ www.cs.sunysb.edu/ skiena/shorty/. Uses paired-read info to create new seeds to crystallize around.
Figures - ETC: Extender of Terminated Contigs
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ETC: Extender of Terminated Contigs.
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OpenSequence.org: Publications
http://www.opensequence.org/2009/09/literature-watch.html
The Freedom To Know. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Sergey Ovchinnikov, Hetunandan Kamisetty, and David Baker. Assessing the utility of coevolution-based residue–residue contact predictions in a sequence-and structure-rich era. Hetunandan Kamisetty, Sergey Ovchinnikov, and David Baker. 110, no. 39 (2013): 15674-15679. Sergey Ovchinnikov, Susan E Masta. 31 (12 March 2012). Sergey Ovchinnikov, Mark Fishbein.
OpenSequence.org: Welcome
http://www.opensequence.org/2009/09/news.html
The Freedom To Know. Welcome to OpenSequence.org. A little about me:. My name is Sergey Ovchinnikov. I majored in Micro/Molecular Biology and minored in Chemistry at Portland State University. I am currently a graduate student at University of Washington for the department of Molecular and Cellular Biology. My advisor is David Baker. Co-evolution (GREMLIN) based analysis can be found at OPENSEQ.org. A table, a chair, a bowl of fruit and a violin; what else does a man need to be happy?
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ETC | an everything tcg
Oct 23, 2011. Nov 27, 2011. Please do not take. Layout Template: punk-rose.com. Everything on this site was made by etc.ohexcite.net. ETC is an Everything Trading Card Game! This TCG will revolve around just about anything you want, though we try to focus on nature, objects, food, etc! Feel free take a look around and if you like what you see, join. To comment on updates, please register here. Function eregi() is deprecated in /home/forevertcg/etc.ohexcite.net/cutenews/show news.php. Function eregi() is ...
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ETC: Extender of Terminated Contigs
ETC: Extender of Terminated Contigs. Update (Sept 04, 2010):. Due to fast nature of the field in question, this project has been unfortunately retired. I've updated the paper section of this page to post the latest draft of the paper. If for whatever chance any of the scripts that I have written or any of the information are found of use to someone, this paper may be cited as follows:. PSU McNair Online Journal. Volume 4. Ronald E. McNair Scholars Program. Where I worked with. Multiple methods and algori...
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