Moderator: Michael Dondrup

gravatar for Michael Dondrup
Reputation:
43,790
Status:
Trusted
Location:
Bergen, Norway
Website:
https://licebase.org/
Last seen:
4 hours ago
Joined:
8 years, 4 months ago
Email:
m*******@gmail.com

 

PhD in bioinformatics. Currently Researcher at the Sea Lice Research Centre, responsible for LiceBase, an infrastructure for genomic resources of sea lice, and analysis of genomics data from emerging genomes.

Posts by Michael Dondrup

<prev • 4,833 results • page 1 of 484 • next >
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Answer: A: perl compilation errors
... What should you do about it? I'd strongly recommend not to use so complex perl one-liners. while some might have a habit of using these to show off how smart a hacker they are, they are the opposite of smart. Using these for more than a few commands is definitely not a good idea, except for making ...
written 11 days ago by Michael Dondrup44k
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Answer: A: How to create a faster way to match a list of string to a list of patterns in r?
... Is this trying to select some sample information? Is the pattern a regular expression? If not: See `?pmatch` or as simple as: pmatch(pattern.list, my.string.vector); This might do it, but I am not totally sure which output format you want, then maybe grep or grepl will provide more control. ...
written 24 days ago by Michael Dondrup44k
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Comment: C: fasta to gff3
... Dear kelishady, welcome to biostars Unfortunately, it is unclear what you are asking the reason for this being that have not invested the appropriate amount of effort. It is highly appreciated that other users are willing to put their precious time into answering even these kind of questions! Howev ...
written 25 days ago by Michael Dondrup44k
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Comment: C: How to map sub-cellular localisation to enteries in uniprot database fasta file.
... I changed the protocol to HTTPS, otherwise the response could be empty, because Uniprot move to https and sends a document moved header. ...
written 25 days ago by Michael Dondrup44k
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Comment: C: Extracting Sub-cellular location from Uniprot into tabular format
... The associations are unfortunately incomplete too. An example: https://www.uniprot.org/uniprot/Q7Q6R1 has only automatic IEA GO annotations that are omitted by AmiGO and therefore nothing is found, but a manual annotation exists anyway in the Uniprot profile of this protein. Likely we will need htt ...
written 25 days ago by Michael Dondrup44k
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Comment: C: Which truseq trimmomatic adapters file to use when removing truseq adapters?
... The best way to know for sure is to ask the sequencing facility. They should provide you with that information as a customer service. Often the standard adapters might work, but sometimes they might have used their own modifications. Whenever we receive a sample I do this. Second best option is to c ...
written 25 days ago by Michael Dondrup44k
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Comment: C: csv file, columns issue
... Hi Jim, please explain the connection to bioinformatics, your question is solved by trivial text processing () and is not a good fit for this site. ...
written 25 days ago by Michael Dondrup44k
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Comment: C: appropriate script for DNA alignment
... Just to give the context> https://www.biostars.org/p/322689/ is related and describes a little bit more how the reference is created. You should really provide us with the context by yourself. Please take a few minutes to edit and revise your post to contain all the necessary information. Pleas ...
written 25 days ago by Michael Dondrup44k
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Answer: A: Extracting Sub-cellular location from Uniprot into tabular format
... So I got a solution using SQL. First, it looks like [assocdb generated by AmiGO][1] is as close as it gets to what I want. This database associates "termdb (above); all manual gene product annotations; electronic annotations (IEA) from all databases other than UniProtKB". 1. Download the weekly b ...
written 26 days ago by Michael Dondrup44k
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Extracting Sub-cellular location from Uniprot into tabular format
... Hi, here's a question which seems more tricky to solve than it looks initially. I am trying to convert SwissProt accessions into a tabular format for import into SQL containing the "best bet" sub-cellular localization of all proteins (one row per pair (accession, location) ): Accession Loca ...
swissprot uniprot parsing written 27 days ago by Michael Dondrup44k • updated 24 days ago by Elisabeth Gasteiger1.5k

Latest awards to Michael Dondrup

Good Answer 20 days ago, created an answer that was upvoted at least 5 times. For A: Clustering Data (Rna-Seq) Using R To Produce A Heatmap
Scholar 26 days ago, created an answer that has been accepted. For A: Extracting Sub-cellular location from Uniprot into tabular format
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: What Does Bwa'S '-N' Parameter Mean?
Scholar 5 weeks ago, created an answer that has been accepted. For A: How To Deal With Duplicate Row Names Error In R
Scholar 5 weeks ago, created an answer that has been accepted. For A: How To Deal With Duplicate Row Names Error In R
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: What Does Bwa'S '-N' Parameter Mean?
Scholar 9 weeks ago, created an answer that has been accepted. For A: Filling expr matrix for igraph
Great Question 9 weeks ago, created a question with more than 5,000 views. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How Do I Access And Query Entire Genome Sequences With R
Scholar 12 weeks ago, created an answer that has been accepted. For A: Filling expr matrix for igraph
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: How To Learn To Build A Bioinformatics Oriented Web Site
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: What Does Bwa'S '-N' Parameter Mean?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How To Learn To Build A Bioinformatics Oriented Web Site
Scholar 4 months ago, created an answer that has been accepted. For A: Filling expr matrix for igraph
Great Question 4 months ago, created a question with more than 5,000 views. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Are There Internships In Bioinformatics? How Can A Foreign Student Get Started I
Great Question 4 months ago, created a question with more than 5,000 views. For Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: How To Find Novel Genes From Comparative Transcriptomics?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?

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