User: Joseph Hughes
Joseph Hughes • 2.7k
- Reputation:
- 2,690
- Status:
- Trusted
- Location:
- Scotland, UK
- Website:
- http://www.bioinformat...
- Twitter:
- blJOg
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 days, 13 hours ago
- Joined:
- 9 years, 2 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
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... What do you mean by information? Entropy? ...
written 26 days ago by
Joseph Hughes • 2.7k
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... 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 ...
written 26 days ago by
Joseph Hughes • 2.7k
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... ****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 ...
written 3 months ago by
Joseph Hughes • 2.7k
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... **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 ...
written 3 months ago by
Joseph Hughes • 2.7k
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... It doesn't like the ":" in your taxa name. ...
written 4 months ago by
Joseph Hughes • 2.7k
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... The format of the sequences and the identifiers in out_ecoli and out_salmonella should enable you to determine that. ...
written 4 months ago by
Joseph Hughes • 2.7k
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... How about expression atlas: https://www.ebi.ac.uk/gxa/home ...
written 4 months ago by
Joseph Hughes • 2.7k
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... You could use [compseq][1] from EMBOSS, you can get the observed and expected of each dinucleotide. Or if you are looking for CpG islands, use [newcpgreport][2]. EMBOSS accepts fasta as an input format.
[1]: http://emboss.sourceforge.net/apps/cvs/emboss/apps/compseq.html
[2]: http://emboss.sour ...
written 4 months ago by
Joseph Hughes • 2.7k
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... Using the [boot.phylo][1] function in the ape package in R, you can do the following:
data(woodmouse)
fun <- function(x) as.phylo(hclust(dist.dna(x), "average"))
tree <- fun(woodmouse)
bstrees <- boot.phylo(tree, woodmouse, fun, trees = TRUE)$trees
boot <- prop.clade ...
written 4 months ago by
Joseph Hughes • 2.7k
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... It is unclear whether you have reads that are interlaced or joined. If you have joined the reads together because they overlap, then these new merged reads can be specfied as a single-end reads along with the other paired-end reads:
spades.py -1 read1.fq -2 read2.fq -s merged.fq -o spades_test
...
written 4 months ago by
Joseph Hughes • 2.7k
Latest awards to Joseph Hughes
Great Question
3 days ago,
created a question with more than 5,000 views.
For Reference Assembly - Mapping Reads To A Reference Genome
Great Question
13 days ago,
created a question with more than 5,000 views.
For Reference Assembly - Mapping Reads To A Reference Genome
Appreciated
13 days ago,
created a post with more than 5 votes.
For A: Plotting Species Distribution Of Proteins
Popular Question
5 weeks ago,
created a question with more than 1,000 views.
For How to check the type of identifier from ensembl?
Popular Question
3 months ago,
created a question with more than 1,000 views.
For How to check the type of identifier from ensembl?
Scholar
4 months ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Scholar
8 months ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
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10 months ago,
created a question with more than 1,000 views.
For DEADLINE 18th of March: 2nd Annual Training Course on Viral Bioinformatics and Genomics
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Plotting Species Distribution Of Proteins
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12 months ago,
created a question with more than 1,000 views.
For DEADLINE 18th of March: 2nd Annual Training Course on Viral Bioinformatics and Genomics
Popular Question
13 months ago,
created a question with more than 1,000 views.
For DEADLINE 18th of March: 2nd Annual Training Course on Viral Bioinformatics and Genomics
Appreciated
14 months ago,
created a post with more than 5 votes.
For A: Plotting Species Distribution Of Proteins
Scholar
16 months ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Student
17 months ago,
asked a question with at least 3 up-votes.
For What Is The Best Search Engine To Use In Repeatmasker?
Appreciated
19 months ago,
created a post with more than 5 votes.
For A: Plotting Species Distribution Of Proteins
Scholar
19 months ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Popular Question
19 months 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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20 months 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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22 months ago,
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For Using Ensembl API to get a Gene ID from a protein ID
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2.0 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
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created an answer that was upvoted at least 5 times.
For A: Plotting Species Distribution Of Proteins
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For How To Find The Nearest Gene To A Retrotransposon Insert?
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Teacher
2.3 years ago,
created an answer with at least 3 up-votes.
For A: Plotting Species Distribution Of Proteins
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Two Bioinformatician Job Openings At The Mrc - University Of Glasgow Centre For Virus Research
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