User: Joseph Hughes

gravatar for Joseph Hughes
Joseph Hughes2.7k
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

<prev • 242 results • page 1 of 25 • next >
0
votes
0
answers
167
views
0
answers
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 26 days ago by Joseph Hughes2.7k
0
votes
0
answers
167
views
0
answers
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 26 days ago by Joseph Hughes2.7k
1
vote
0
answers
296
views
0
answers
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 3 months ago by Joseph Hughes2.7k
0
votes
0
answers
844
views
0
answers
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 3 months ago by Joseph Hughes2.7k
0
votes
1
answer
218
views
1
answers
Answer: A: Phylonet -a taxa map parameter
... It doesn't like the ":" in your taxa name. ...
written 4 months ago by Joseph Hughes2.7k
1
vote
1
answer
398
views
1
answers
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 4 months ago by Joseph Hughes2.7k
0
votes
2
answers
382
views
2
answers
Answer: A: Any database for downloading cancer cell-lines transcriptome differential expres
... How about expression atlas: https://www.ebi.ac.uk/gxa/home ...
written 4 months ago by Joseph Hughes2.7k
0
votes
3
answers
333
views
3
answers
Answer: A: How calculate CG content for each contig in an transcript assembly?
... 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 Hughes2.7k
2
votes
2
answers
244
views
2
answers
Answer: A: plot and show support values in consensus tree from n nj euclidean distance matr
... 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 Hughes2.7k
1
vote
1
answer
398
views
1
answers
Answer: A: How to give merged reads as input in spades
... 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 Hughes2.7k

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
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
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
Popular Question 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
Popular Question 22 months 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 2.0 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 2.0 years ago, 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 928 users visited in the last hour