User: Joseph Hughes

gravatar for Joseph Hughes
Joseph Hughes2.5k
Reputation:
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Trusted
Location:
Scotland, UK
Website:
http://www.bioinformat...
Twitter:
blJOg
Scholar ID:
Google Scholar Page
Last seen:
1 day, 18 hours ago
Joined:
7 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

<prev • 227 results • page 1 of 23 • next >
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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 12 days ago by Joseph Hughes2.5k
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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 23 days ago by Joseph Hughes2.5k
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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 26 days ago by Joseph Hughes2.5k
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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 27 days ago by Joseph Hughes2.5k
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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 27 days ago by Joseph Hughes2.5k
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Comment: C: LoFreq outputing no SNP?
... You could try without the automatic lofreq filtering: --no-default-filter ...
written 28 days ago by Joseph Hughes2.5k
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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 4 weeks ago by Joseph Hughes2.5k
0
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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 4 weeks ago by Joseph Hughes2.5k
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Answer: A: To get the name of the strains by searching assembly genome number GCF_
... Re-writting the following query in python should get you what you want: esearch -db assembly -query "GCF_002514765.1" | esummary | xtract -pattern DocumentSummary -element SpeciesName Sub_type Sub_value The output is: Escherichia coli strain MOD1-EC3823 ...
written 4 weeks ago by Joseph Hughes2.5k
0
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Comment: C: How to retrieve nucleotid sequence from gene ids of ncbis "gene" data base?
... Does your starting point have to be the taxid? The problem with starting with a taxid is that it is not very precise. It sounds like you know the two full reference genomes that you want to extract genes from so why not start from those accession numbers? ...
written 4 weeks ago by Joseph Hughes2.5k

Latest awards to Joseph Hughes

Scholar 28 days ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Student 6 weeks ago, asked a question with at least 3 up-votes. For What Is The Best Search Engine To Use In Repeatmasker?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Scholar 3 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
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
Popular Question 4 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 6 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 8 months ago, created an answer that was upvoted at least 5 times. For A: Plotting Species Distribution Of Proteins
Popular Question 8 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 9 months ago, created a question with more than 1,000 views. For How To Find The Nearest Gene To A Retrotransposon Insert?
Scholar 9 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Teacher 12 months ago, created an answer with at least 3 up-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
Scholar 13 months ago, created an answer that has been accepted. For A: Phylogenetic tree for 16S rRNA with whole taxonomy included
Scholar 14 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 Which simulator to use for generating fastq reads from a population of haploids
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Plotting Species Distribution Of Proteins
Popular Question 17 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 21 months ago, created a post with more than 5 votes. For A: Plotting Species Distribution Of Proteins
Gold Standard 22 months ago, created a post with more than 25 bookmarks. For Reference Assembly - Mapping Reads To A Reference Genome
Great Question 22 months ago, created a question with more than 5,000 views. For Help With Understanding The Output Of Codeml From The Paml Package
Student 22 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 Why Shouldn'T I Use Masking When Doing A Reference Alignment?

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