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User: Joseph Hughes

gravatar for Joseph Hughes
Joseph Hughes • 2.1k
Reputation:
2,140
Status:
Trusted
Location:
Scotland, UK
Website:
http://www.bioinformat...
Twitter:
blJOg
Scholar ID:
Google Scholar Page
Last seen:
1 week, 2 days ago
Joined:
7 years, 6 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 • 199 results • page 1 of 20 • next >
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Answer: A: findMotifsGenome.pl Homer using "RNA"
... I think you need to use -rna, it looks like you are forgetting the hyphen. From the website: Search for RNA motifs ("-rna") If looking at RNA data (i.e. Clip-Seq or similar), this option will restrict HOMER to only search the + strand (relative to the peak), and will output RNA motif logos (i.e. ...
written 10 days ago by Joseph Hughes • 2.1k
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Answer: A: To retrieve bacterial Phylum and Class information from a set of tax id
... You could use NCBI eutilities with esarch and efetch. From the xml output you can extract the full lineage: esearch -db taxonomy -query "txid11053 [Organism]" | efetch -format xml | xtract -element Lineage ...
written 10 days ago by Joseph Hughes • 2.1k
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Job: Bioinformatician/Biological Data Scientist - two posts : Glasgow, United KingdomJOB: https://www.nature.com/naturejobs/science/jobs/623965-bioinformatician-biological-data-scientist-two-posts
... We are seeking to appoint two biological data scientists/computational biologists to join our expanding bioinformatics team and enhance the research activities of the MRC-University of Glasgow Centre for Virus Research (CVR) (http://www.cvr.ac.uk/). CVR Bioinformatics comprises a large team of MRC-f ...
bioinformatician job virus written 11 days ago by Joseph Hughes • 2.1k
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Comment: C: Distance matrix plot issue
... Perhaps you can post your own answer to your question for the next person who has the same issue. ...
written 9 weeks ago by Joseph Hughes • 2.1k
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Comment: C: Adaptors Sequences and Trimming
... If you received lots of good help last time, perhaps you should up vote the responses and comments you got and accept the answers that worked for you. ...
written 9 weeks ago by Joseph Hughes • 2.1k
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Answer: A: Pseudogene identification and classification
... There is a tool called PseudoGeneQuest but the webserver seems to be down or no longer functional: [http://bioinf.uta.fi/PseudoGeneQuest][1] The article is here: [PseudoGeneQuest – Service for identification of different pseudogene types in the human genome][2] [1]: http://bioinf.uta.fi/PseudoG ...
written 9 weeks ago by Joseph Hughes • 2.1k
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Answer: A: Distance matrix plot issue
... Going through the examples for [heatmap.2][1] should enable you to do what you want. [1]: https://www.rdocumentation.org/packages/gplots/versions/3.0.1/topics/heatmap.2 ...
written 9 weeks ago by Joseph Hughes • 2.1k
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Answer: A: Phylogenetic tree support for a user-defined partition
... There are several ways of doing this phylogenetically. You could for example constrain the topology with X as part of clade A and caulclate the likelihood of the tree, then repeat for X as part of B and then do a likelihood ratio test to see whether the trees are significantly different. You can do ...
written 3 months ago by Joseph Hughes • 2.1k
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Answer: A: Issues with executing on Nexus files with MrBayes
... You are missing a semi-colon ";" at the end of the file. ...
written 4 months ago by Joseph Hughes • 2.1k
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Answer: A: 'ORIGIN' flag missing in GenBank files
... How about trying something like this: esearch -db assembly -query "Homo sapiens[ORGN] AND latest[SB]" | efetch -format docsum | xtract -pattern DocumentSummary -element AssemblyAccession SpeciesTaxid SpeciesName FtpPath_RefSeq | sed 's/,.*//' | sort -k 3,3 | tee downloaded_genomes.tsv | cut -f ...
written 4 months ago by Joseph Hughes • 2.1k

Latest awards to Joseph Hughes

Popular Question 8 weeks 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 months 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 months ago, created an answer that was upvoted at least 5 times. For A: Plotting Species Distribution Of Proteins
Popular Question 4 months ago, created a question with more than 1,000 views. For How To Find The Nearest Gene To A Retrotransposon Insert?
Scholar 4 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Popular Question 7 months 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
Popular Question 7 months 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 8 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Scholar 8 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Scholar 9 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Popular Question 10 months ago, created a question with more than 1,000 views. For Which simulator to use for generating fastq reads from a population of haploids
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Popular Question 12 months ago, created a question with more than 1,000 views. For Which simulator to use for generating fastq reads from a population of haploids
Appreciated 16 months ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Great Question 17 months ago, created a question with more than 5,000 views. For Help With Understanding The Output Of Codeml From The Paml Package
Gold Standard 17 months ago, created a post with more than 25 bookmarks. For Reference Assembly - Mapping Reads To A Reference Genome
Popular Question 17 months ago, created a question with more than 1,000 views. For Why Shouldn'T I Use Masking When Doing A Reference Alignment?
Student 17 months ago, asked a question with at least 3 up-votes. For How To Find The Nearest Gene To A Retrotransposon Insert?
Popular Question 22 months ago, created a question with more than 1,000 views. For Reference Assembly - Mapping Reads To A Reference Genome
Popular Question 23 months ago, created a question with more than 1,000 views. For Reference Assembly - Mapping Reads To A Reference Genome
Epic Question 24 months ago, created a question with more than 10,000 views. For Reference Assembly - Mapping Reads To A Reference Genome
Popular Question 2.2 years ago, created a question with more than 1,000 views. For What Is The Best Search Engine To Use In Repeatmasker?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Why Shouldn'T I Use Masking When Doing A Reference Alignment?
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