User: Erik Wright

gravatar for Erik Wright
Erik Wright360
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360
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Website:
http://DECIPHER.codes/
Last seen:
9 months, 2 weeks ago
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3 years, 7 months ago
Email:
d************@gmail.com

Posts by Erik Wright

<prev • 28 results • page 1 of 3 • next >
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Job: Postdoc: Investigating thousands of microbial genomes with novel bioinformatics approaches (University of Pittsburgh)
... What power is there in having access to thousands of genomes over a single genome of a species? The Wright Lab (http://wrightlabscience.com) is seeking an enthusiastic postdoctoral scholar to answer this question using thousands of microbial genomes. The successful candidate will develop and evaluat ...
postdoc evolution job genomics microbiome written 9 months ago by Erik Wright360
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Answer: A: Bioinformatic Algorithms Books
... Here is another option: [Algorithms on strings, trees, and sequences][1] [1]: https://www.amazon.com/Algorithms-Strings-Trees-Sequences-Computational/dp/0521585198 ...
written 2.8 years ago by Erik Wright360
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Answer: A: How to draw a phylogenetic tree together with a genome locus structure?
... You might take a look at [facet_plot][1]. [1]: https://www.r-bloggers.com/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A%20RBloggers%20%28R%20bloggers%29 ...
written 2.8 years ago by Erik Wright360
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Comment: C: Checking primers against many target genes, with mismatch tolerance
... Hi John, As you pointed out, there is a mismatch cutoff built into the program. The user can specify a different cutoff, but I gather that is not the point you are trying to make. Have you tried your example primer with your example template in a PCR reaction at the conditions you specified? And ...
written 2.8 years ago by Erik Wright360
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Comment: C: Checking primers against many target genes, with mismatch tolerance
... The amplification efficiency model is published in: ES Wright et al. (2013) "Exploiting Extension Bias in PCR to Improve Primer Specificity in Ensembles of Nearly Identical DNA Templates." Environmental Microbiology, doi:10.1111/1462-2920.12259. Indeed, the efficiency of a primer set (forward and ...
written 2.8 years ago by Erik Wright360
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Comment: C: Checking primers against many target genes, with mismatch tolerance
... Hi Rotem, I am glad it is working for you. The current output does not include which template amplified in the DNAStringSet. It simply gives the predicted amplification efficiency followed by the primer set (1 x 2 = 1st and 2nd) for each amplicon. I might add your requested feature in a future v ...
written 2.8 years ago by Erik Wright360
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Comment: C: Checking primers against many target genes, with mismatch tolerance
... Hi Rotem, You will need to install OligoArrayAux as the documentation says. This only requires a C compiler such as gcc. Xcode is one option, and you can always remove the Xcode application after it installs the necessary tools (simply delete it). ...
written 2.8 years ago by Erik Wright360
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Answer: A: Programs for RNA secondary structure predictions
... Consensus RNA secondary structure can be predicted from a sequence alignment using the [DECIPHER][1] package for **R**: rna <- readRNAStringSet("<>") ?PredictDBN # opens helpful information p <- PredictDBN(rna, "states") I hope that helps! [1]: http://DECIPHER.codes ...
written 2.8 years ago by Erik Wright360
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Answer: A: Checking primers against many target genes, with mismatch tolerance
... You can confirm specificity and sensitivity of primers using the **R** package [DECIPHER][1]. It uses a model of hybridization and elongation efficiency based on the location and type of mismatches. For example: library(DECIPHER) ?AmplifyDNA # displays helpful information dna <- re ...
written 2.8 years ago by Erik Wright360
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Comment: C: PhD programs in bioinformatics and genomics
... You can download publication data (including author affiliations) from [PubMed][1]. [1]: https://www.ncbi.nlm.nih.gov/pubmed/?term=%22Briefings%20in%20bioinformatics%22%5BJournal%5D%20OR%20%22Bioinformatics%22%5BJournal%5D%20OR%20%22PLOS%20Computational%20Biology%22%5BJournal%5D%20OR%20%22Nuclei ...
written 2.9 years ago by Erik Wright360

Latest awards to Erik Wright

Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: PhD programs in bioinformatics and genomics
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: read FASTA file in R, including description information
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: PhD programs in bioinformatics and genomics
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: All completed genomes for a phyla
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: PhD programs in bioinformatics and genomics
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: All completed genomes for a phyla
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: All completed genomes for a phyla
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: All completed genomes for a phyla
Scholar 3.6 years ago, created an answer that has been accepted. For A: All completed genomes for a phyla
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: All completed genomes for a phyla

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