User: Joseph Hughes

gravatar for Joseph Hughes
Joseph Hughes2.9k
Reputation:
2,850
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Location:
Scotland, UK
Website:
http://www.bioinformat...
Twitter:
blJOg
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Google Scholar Page
Last seen:
1 week, 3 days ago
Joined:
10 years, 10 months ago
Email:
h************@gmail.com

My interests are in the evolution of host-parasite interactions. Phylogenetics and bioinformatics form an important aspect of my research. You can see my most recent publications http://www.mendeley.com/profiles/joseph-hughes/ http://twitter.com/blJOg

Posts by Joseph Hughes

<prev • 247 results • page 1 of 25 • next >
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Comment: C: How to download sequence of a protein from all available species from NCBI?
... You can use the package Rentrez in R with a similar syntax to what @GenoMax suggested. ...
written 10 days ago by Joseph Hughes2.9k
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Comment: C: Do I need to search for the complementary sequence when using regex?
... If you mean you are searching in fast sequence of a contig or a consensus sequence, then yes you will need to search for both. Generally if producing an assembly using denovo tools, the program will not know what is the correct 5' to 3' etc... If you are searching in a SAM/BAm of aligned reads again ...
written 10 days ago by Joseph Hughes2.9k
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Answer: A: Viral genome annotation
... Viruses are super diverse and range hugely in size and the number of genes. Tools that I have found useful for annotation of viruses are RATT, VaPiD and VGas. Each has pros and cons. I would maybe suggest starting with VAPiD but then I am not too sure what your data is like, specifically how novel y ...
written 14 months ago by Joseph Hughes2.9k
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Answer: A: calculating confidence intervals of boostrapped trees
... In PAUP, you can summarise your jacknife trees either on the majority rule tree or on a constraint tree of your choice that you provide to it. You can also use SumTrees, part of the Dendropy python package or the APE package in R to do the same thing. You can also do something similar if you have ...
written 14 months ago by Joseph Hughes2.9k
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In the reformat tool of BBmap what is the meaning of Read1_linear and Read1_log
... This is an example output from bbmap's reformat.sh tool using the following command: reformat.sh in1=input_R1.fq in2=input_R2.fq qhist=quality.txt I've looked on the [website][1] and search biostars and seqanswers to try to understand what the column labels mean, with no luck. #BaseNum R ...
reads quality bbmap written 16 months ago by Joseph Hughes2.9k • updated 16 months ago by h.mon32k
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Comment: C: Is there a way to calculate the maximum length at which the frequencies of k-mer
... What do you mean by information? Entropy? ...
written 20 months ago by Joseph Hughes2.9k
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Is there a way to calculate the maximum length at which the frequencies of k-mers can be accurately estimated?
... A reviewer has asks us to calculate the theoretical range of optimal k-mer sizes for a given database of viral sequences, stating: "The optimal range lies between: the minimum size for which a maximum number of different features can be found in the string (the viral genome); and the maximum length ...
k-mer frequency written 20 months ago by Joseph Hughes2.9k
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Job: Deadline 26th of March: Research Database Curator
... ****Research Database Curator** **Vacancy Ref: 024569** **Grade 6: £28,660 - £32,236 per annum, pro rata for 20 hours per week** **This post is part time (20 hours per week) and has funding until 31 March 2020.**** The MRC-University of Glasgow Centre for Virus Research (CVR) (http://www.cvr ...
data bioinfromatics hcv job curator virus written 22 months ago by Joseph Hughes2.9k
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Job: Bioinformatician position at the Centre for Virus Research - Glasgow, UK
... **Bioinformatician** **Closing date for application: 14th of March** Reference Number 024544 Location Garscube Campus College / Service COLLEGE OF MVLS Department RI INFECTION IMMUNITY & INFLAMMATION Job Family Research And Teaching Position Type Full Time Salary Range £28,660 - £32,236 Job Pu ...
phylogenetics evolution hiv outbreak job written 23 months ago by Joseph Hughes2.9k
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Answer: A: Phylonet -a taxa map parameter
... It doesn't like the ":" in your taxa name. ...
written 24 months ago by Joseph Hughes2.9k

Latest awards to Joseph Hughes

Great Question 6 months ago, created a question with more than 5,000 views. For Which simulator to use for generating fastq reads from a population of haploids
Appreciated 13 months ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Good Question 15 months ago, asked a question that was upvoted at least 5 times. For When Is The Best Time To Submit Sequences To Public Databases Like Ncbi?
Popular Question 15 months ago, created a question with more than 1,000 views. For How to check the type of identifier from ensembl?
Popular Question 15 months ago, created a question with more than 1,000 views. For How to check the type of identifier from ensembl?
Great Question 19 months ago, created a question with more than 5,000 views. For Reference Assembly - Mapping Reads To A Reference Genome
Appreciated 19 months ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Great Question 19 months ago, created a question with more than 5,000 views. For Reference Assembly - Mapping Reads To A Reference Genome
Popular Question 20 months ago, created a question with more than 1,000 views. For How to check the type of identifier from ensembl?
Popular Question 22 months ago, created a question with more than 1,000 views. For How to check the type of identifier from ensembl?
Scholar 24 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Scholar 2.3 years ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Scholar 3.0 years ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Student 3.0 years ago, asked a question with at least 3 up-votes. For What Is The Best Search Engine To Use In Repeatmasker?
Scholar 3.2 years ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Using Ensembl API to get a Gene ID from a protein ID
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Using Ensembl API to get a Gene ID from a protein ID
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Using Ensembl API to get a Gene ID from a protein ID

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