User: terdon

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terdon410
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Posts by terdon

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Remove optical duplicates from bam file
... Thanks for all your work, Anna! Sorry to bug you but is there any news on this? Can we now trust MarkDuplicates in, for example, version 2.01? ...
written 3.3 years ago by terdon410
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Answer: A: Need Help In Protein Protein Interaction
... You can't. The best you can do is check if both interacting partners are part of the same pathway. However, you can have a pathway like the following: A => B => C If you find an interaction between A and C, you have no way of knowing if that interaction has anything to do with the pathway t ...
written 6.1 years ago by terdon410
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Comment: C: Convert Refseq Id To Gene Name
... Of course we do, which is why we don't use Excel :). ...
written 6.1 years ago by terdon410
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Comment: C: What Percentage Of Protein Isoforms Have Different Functions?
... Well, changes in UTRs do not result in different protein isoforrms, so that doesn't really enter into it. As for which and why, it depends in what you consider different functions. The different isoforms could just have a different pH sensitivity but catalyze the same reaction, or they could have d ...
written 6.2 years ago by terdon410
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Comment: C: What Percentage Of Protein Isoforms Have Different Functions?
... Thanks, I'll have a look at the papers. As for Uniprot, you're exactly right, they have the number of isoforms and in some cases different functions but not always and not organized in any meaningful way. ...
written 6.2 years ago by terdon410
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Comment: C: Unique-Ify The Contents Of A Fasta-Formatted File And Associated Read Numbers
... You are assuming that every sequence will be very short, your paste command will break on longer ones. Also, there is no need to use cat, just run paste - - your.fa | perl .... ...
written 6.2 years ago by terdon410
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Comment: C: What Percentage Of Protein Isoforms Have Different Functions?
... Yup, exactly, that's what I want to analyze. My first step though is to see how often different isoforms are annotated to different functions and I can't figure out where to get that information because too many of the high-troughput functional assays are gene based. ...
written 6.2 years ago by terdon410
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What Percentage Of Protein Isoforms Have Different Functions?
... I am looking for studies on how many protein isoforms have different functions, preferably in human. We know that a great many, if not most, of human genes are alternatively spliced and that many produce different protein isoforms. Has anyone looked at how many of these isoforms have different cellu ...
function protein human written 6.2 years ago by terdon410 • updated 6.2 years ago by Mary11k
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Comment: C: How To Visualize Gene Fusions To Better Illustrate The Gene Structure?
... It really is a great tool once you manage to get it to work. The documentation is really hard though. When I used to work with him, we would always just ask the author to sort it out for us :). On the bright side, it is open source and written in Perl so it is editable. ...
written 6.3 years ago by terdon410
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Answer: A: How To Visualize Gene Fusions To Better Illustrate The Gene Structure?
... I'm not sure how it deals with fusions but gff2ps is a great tool for this kind of visualization. It was used to produce the images and printable posters for the Celera Human Genome assembly. It is, admittedly, not very easy to use but incredibly powerful. Having spent a few years working next to it ...
written 6.3 years ago by terdon410

Latest awards to terdon

Great Question 5 months ago, created a question with more than 5,000 views. For How Can I Compare Rates Of Evolution For Two Sets Of Genes?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Extracting Columns From Csv File And Puting It In An Perl Array Data Type.
Commentator 3.3 years ago, created a comment with at least 3 up-votes. For C: Convert Refseq Id To Gene Name
Student 3.3 years ago, asked a question with at least 3 up-votes. For What Percentage Of Protein Isoforms Have Different Functions?
Popular Question 5.2 years ago, created a question with more than 1,000 views. For How Can I Compare Rates Of Evolution For Two Sets Of Genes?
Popular Question 5.2 years ago, created a question with more than 1,000 views. For What Percentage Of Protein Isoforms Have Different Functions?
Appreciated 5.3 years ago, created a post with more than 5 votes. For A: How To Visualize Gene Fusions To Better Illustrate The Gene Structure?
Appreciated 5.3 years ago, created a post with more than 5 votes. For A: Extracting Columns From Csv File And Puting It In An Perl Array Data Type.
Appreciated 5.3 years ago, created a post with more than 5 votes. For What Percentage Of Protein Isoforms Have Different Functions?
Good Question 5.3 years ago, asked a question that was upvoted at least 5 times. For What Percentage Of Protein Isoforms Have Different Functions?
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: How To Visualize Gene Fusions To Better Illustrate The Gene Structure?
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: Extracting Columns From Csv File And Puting It In An Perl Array Data Type.
Teacher 5.3 years ago, created an answer with at least 3 up-votes. For A: Why Does A Psi-Blast Search Produce Fewer Hits On Subsequent Iterations?
Student 5.3 years ago, asked a question with at least 3 up-votes. For What Percentage Of Protein Isoforms Have Different Functions?

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