User: Joseph Hughes
Joseph Hughes • 2.7k
- Reputation:
- 2,660
- Status:
- Trusted
- Location:
- Scotland, UK
- Website:
- http://www.bioinformat...
- Twitter:
- blJOg
- Scholar ID:
- Google Scholar Page
- Last seen:
- 2 days ago
- Joined:
- 8 years, 11 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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... It doesn't like the ":" in your taxa name. ...
written 23 days 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 28 days ago by
Joseph Hughes • 2.7k
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... How about expression atlas: https://www.ebi.ac.uk/gxa/home ...
written 4 weeks 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 weeks 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 weeks 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 weeks ago by
Joseph Hughes • 2.7k
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... Are you talking about MG-RAST? ...
written 4 weeks ago by
Joseph Hughes • 2.7k
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... I'm not having much luck running iAssembler. At the moment, I'm thinking of doing a de-novo transcriptome assembly with Trinity and then using CPA3 to merge my ESTs with the trinity-assembled transcripts. ...
written 4 weeks ago by
Joseph Hughes • 2.7k
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... I am trying to improve the annotations in a region of the Sheep genome and have compiled at set of 60 Sanger sequenced ESTs from sheep which I would like to assemble with a set of 2,863,891 sheep Illumina reads from a transcriptomic study. These are the reads that mapped to a syntenic region in the ...
written 4 weeks ago by
Joseph Hughes • 2.7k
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... Perhaps, something like [genoplotR][1] would do the trick. I found it useful for looking at synteny of genes in large virus genomes.
[1]: http://genoplotr.r-forge.r-project.org/ ...
written 12 weeks ago by
Joseph Hughes • 2.7k
Latest awards to Joseph Hughes
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4 weeks ago,
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For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Scholar
4 months ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Popular Question
7 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
7 months ago,
created an answer with at least 3 up-votes.
For A: Plotting Species Distribution Of Proteins
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8 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
9 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
11 months ago,
created a post with more than 5 votes.
For A: Plotting Species Distribution Of Proteins
Scholar
13 months ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Student
13 months ago,
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For What Is The Best Search Engine To Use In Repeatmasker?
Appreciated
15 months ago,
created a post with more than 5 votes.
For A: Plotting Species Distribution Of Proteins
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15 months ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Popular Question
15 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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For Using Ensembl API to get a Gene ID from a protein ID
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19 months ago,
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For Using Ensembl API to get a Gene ID from a protein ID
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20 months ago,
created an answer that was upvoted at least 5 times.
For A: Plotting Species Distribution Of Proteins
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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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21 months ago,
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For How To Find The Nearest Gene To A Retrotransposon Insert?
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22 months ago,
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For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Teacher
24 months ago,
created an answer with at least 3 up-votes.
For A: Plotting Species Distribution Of Proteins
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2.0 years ago,
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For Two Bioinformatician Job Openings At The Mrc - University Of Glasgow Centre For Virus Research
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2.0 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
Teacher
2.1 years ago,
created an answer with at least 3 up-votes.
For A: Plotting Species Distribution Of Proteins
Scholar
2.1 years ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Scholar
2.2 years ago,
created an answer that has been accepted.
For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For Which simulator to use for generating fastq reads from a population of haploids
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