User: Joseph Hughes

gravatar for Joseph Hughes
Joseph Hughes2.8k
Reputation:
2,790
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Location:
Scotland, UK
Website:
http://www.bioinformat...
Twitter:
blJOg
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Google Scholar Page
Last seen:
1 month ago
Joined:
10 years, 4 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 • 245 results • page 1 of 25 • next >
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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 9 months ago by Joseph Hughes2.8k
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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 9 months ago by Joseph Hughes2.8k
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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 11 months ago by Joseph Hughes2.8k • updated 11 months ago by h.mon30k
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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 14 months ago by Joseph Hughes2.8k
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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 14 months ago by Joseph Hughes2.8k
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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 17 months ago by Joseph Hughes2.8k
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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 17 months ago by Joseph Hughes2.8k
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Answer: A: Phylonet -a taxa map parameter
... It doesn't like the ":" in your taxa name. ...
written 18 months ago by Joseph Hughes2.8k
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Comment: C: How to give merged reads as input in spades
... The format of the sequences and the identifiers in out_ecoli and out_salmonella should enable you to determine that. ...
written 18 months ago by Joseph Hughes2.8k
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Answer: A: Any database for downloading cancer cell-lines transcriptome differential expres
... How about expression atlas: https://www.ebi.ac.uk/gxa/home ...
written 18 months ago by Joseph Hughes2.8k

Latest awards to Joseph Hughes

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Appreciated 8 months ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Popular Question 10 months ago, created a question with more than 1,000 views. For How to check the type of identifier from ensembl?
Good Question 10 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 10 months ago, created a question with more than 1,000 views. For How to check the type of identifier from ensembl?
Great Question 14 months ago, created a question with more than 5,000 views. For Reference Assembly - Mapping Reads To A Reference Genome
Appreciated 14 months ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Great Question 14 months ago, created a question with more than 5,000 views. For Reference Assembly - Mapping Reads To A Reference Genome
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 17 months ago, created a question with more than 1,000 views. For How to check the type of identifier from ensembl?
Scholar 18 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Scholar 22 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Scholar 2.5 years ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Student 2.6 years ago, asked a question with at least 3 up-votes. For What Is The Best Search Engine To Use In Repeatmasker?
Scholar 2.7 years ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Popular Question 2.7 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 2.8 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 3.0 years ago, created a question with more than 1,000 views. For Using Ensembl API to get a Gene ID from a protein ID
Good Answer 3.2 years ago, created an answer that was upvoted at least 5 times. For A: Plotting Species Distribution Of Proteins

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