User: Joseph Hughes
Joseph Hughes • 2.8k
- Reputation:
- 2,790
- Status:
- Trusted
- Location:
- Scotland, UK
- Website:
- http://www.bioinformat...
- Twitter:
- blJOg
- Scholar ID:
- 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
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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 Hughes • 2.8k
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... 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 Hughes • 2.8k
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... 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 ...
written 11 months ago by
Joseph Hughes • 2.8k
• updated
11 months ago by
h.mon ♦ 30k
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... What do you mean by information? Entropy? ...
written 14 months ago by
Joseph Hughes • 2.8k
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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 14 months ago by
Joseph Hughes • 2.8k
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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 17 months ago by
Joseph Hughes • 2.8k
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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 17 months ago by
Joseph Hughes • 2.8k
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... It doesn't like the ":" in your taxa name. ...
written 18 months ago by
Joseph Hughes • 2.8k
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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 18 months ago by
Joseph Hughes • 2.8k
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... How about expression atlas: https://www.ebi.ac.uk/gxa/home ...
written 18 months ago by
Joseph Hughes • 2.8k
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
Popular Question
2.0 years 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
2.1 years ago,
created an answer with at least 3 up-votes.
For A: Plotting Species Distribution Of Proteins
Popular Question
2.2 years 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
2.2 years 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
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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