User: Joseph Hughes

gravatar for Joseph Hughes
Joseph Hughes2.6k
Reputation:
2,610
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Trusted
Location:
Scotland, UK
Website:
http://www.bioinformat...
Twitter:
blJOg
Scholar ID:
Google Scholar Page
Last seen:
2 days, 20 hours ago
Joined:
8 years, 8 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 • 229 results • page 1 of 23 • next >
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Answer: A: Is there a tool for making a synteny blocks of a gene with its downstream and up
... 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 19 days ago by Joseph Hughes2.6k
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Answer: A: Where to get Epimatrix algorithm from for epitope binding prediction?
... The paper that explains how the Epimatrix score matrix is produced, is this one: [https://www.sciencedirect.com/science/article/pii/S0264410X9800173X?via%3Dihub][1] [1]: https://www.sciencedirect.com/science/article/pii/S0264410X9800173X?via%3Dihub ...
written 19 days ago by Joseph Hughes2.6k
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Comment: C: Method for creating an EMBL formatted annotated sequence?
... I think this should work. 1) Convert your BED to GFF using GenomeTools: [http://genometools.org/tools/gt_bed_to_gff3.html][1] 2) Using [seqret][2] from EMBOSS, convert your fasta and gff to embl follwoing this previous post: [https://www.biostars.org/p/72220/][3] Let us know how it goes. [1]: h ...
written 10 months ago by Joseph Hughes2.6k
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Comment: C: How to build an NJ tree with an IBS distance matrix computed by PLINK?
... What does the file look like? ...
written 10 months ago by Joseph Hughes2.6k
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Answer: A: Porting genome annotations from virus RefSeq to new strain: any web tools?
... [RATT][1] is a tool developed by Sanger which works well for annotation transfer from strains and closely related species. You will need an embl formatted file with the annotations and your fasta formatted sequence to start off with. Another tool worth trying but I haven't used is [GATU][2] for whi ...
written 10 months ago by Joseph Hughes2.6k
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Comment: C: kraken: unable to download the databases from ncbi
... I believe Derrick Wood, kraken developer, has moved on to pastures new. ...
written 10 months ago by Joseph Hughes2.6k
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Answer: A: kraken: unable to download the databases from ncbi
... Since NCBI updated their FTP website and decided to phase-out Genbank Identifiers (GIs), the default Kraken database update scripts do not work. My colleague @Sej Modha has written a python script that helps with updating the kraken databases: http://bioinformatics.cvr.ac.uk/blog/update-kraken-data ...
written 10 months ago by Joseph Hughes2.6k
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Comment: C: LoFreq outputing no SNP?
... You could try without the automatic lofreq filtering: --no-default-filter ...
written 10 months ago by Joseph Hughes2.6k
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Comment: C: Bacterial known pathway - the easiest way to find and download 1:1 orthologs to
... This is going to involve parsing the information from the available datasets. I suggest either parsing the "OMA groups" file in txt or xml or the "OMA Groups/Sequences in COGs format". However I could not find the important file listing the Gram positive bacteria. You may need to do this by using th ...
written 10 months ago by Joseph Hughes2.6k
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Comment: C: To get the name of the strains by searching assembly genome number GCF_
... you will need to do a loop in your python code to query each accession one at a time. ...
written 10 months ago by Joseph Hughes2.6k

Latest awards to Joseph Hughes

Scholar 11 weeks ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Teacher 4 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
Scholar 10 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Student 11 months ago, asked a question with at least 3 up-votes. For What Is The Best Search Engine To Use In Repeatmasker?
Scholar 12 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Appreciated 12 months ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Popular Question 13 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 14 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 16 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 18 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 18 months ago, created an answer that was upvoted at least 5 times. For A: Plotting Species Distribution Of Proteins
Popular Question 19 months ago, created a question with more than 1,000 views. For How To Find The Nearest Gene To A Retrotransposon Insert?
Scholar 19 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Scholar 23 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Scholar 2.0 years ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Popular Question 2.1 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
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins

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