User: Joseph Hughes
Joseph Hughes • 2.9k
- Reputation:
- 2,850
- Status:
- Trusted
- Location:
- Scotland, UK
- Website:
- http://www.bioinformat...
- Twitter:
- blJOg
- Scholar ID:
- 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
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... You can use the package Rentrez in R with a similar syntax to what @GenoMax suggested. ...
written 10 days ago by
Joseph Hughes • 2.9k
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... 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 Hughes • 2.9k
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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 Hughes • 2.9k
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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 14 months ago by
Joseph Hughes • 2.9k
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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 16 months ago by
Joseph Hughes • 2.9k
• updated
16 months ago by
h.mon ♦ 32k
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721
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... What do you mean by information? Entropy? ...
written 20 months ago by
Joseph Hughes • 2.9k
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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 20 months ago by
Joseph Hughes • 2.9k
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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 22 months ago by
Joseph Hughes • 2.9k
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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 23 months ago by
Joseph Hughes • 2.9k
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543
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... It doesn't like the ":" in your taxa name. ...
written 24 months ago by
Joseph Hughes • 2.9k
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
Popular Question
2.5 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
2.5 years ago,
created an answer with at least 3 up-votes.
For A: Plotting Species Distribution Of Proteins
Popular Question
2.6 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
2.7 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
2.8 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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