User: Blunders

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Blunders1.1k
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Posts by Blunders

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Comment: C: Consensus Sequence Algorithms And Notation
... @brentp: Thanks, switched my answer selection to you. You might note the output of the script in the answer, since I didn't notice the results of the script until I started reading the code itself -- still super answer, cheers!! ...
written 7.5 years ago by Blunders1.1k
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Comment: C: Consensus Sequence Algorithms And Notation
... +3 @Eric Normandeau: Thanks for all your comments, my question was more of a generalization of the issue, since it's not my problem, it's someone else; just trying to get a feel for it. I in fact am aware of the IUPAC nucleotide codes, and agree that they're a good option - though it still does not ...
written 7.5 years ago by Blunders1.1k
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Comment: C: Consensus Sequence Algorithms And Notation
... @bilouweb: Finally got a chance to look at the link you posted (I was on my phone until now) -- pretty cool, too bad the code for the "adv. consensus" is not open source. Thanks! ...
written 7.5 years ago by Blunders1.1k
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Comment: C: Consensus Sequence Algorithms And Notation
... @Michael Schubert: Thanks, I'd run across the sequence logo when reviewing the wiki for http://en.wikipedia.org/wiki/Consensus_sequence; which appear to be a twist on http://en.wikipedia.org/wiki/Tag_cloud. That's not what I'm looking for, since that's designed main for humans to read, I'm looking m ...
written 7.5 years ago by Blunders1.1k
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Comment: C: Consensus Sequence Algorithms And Notation
... @Eric normandeau: Are you saying the reference sequence would have more weight? If so, how so? Also, the sequences are meant to be examples of distribution in compact form, didn't think bias was given to the stablity of a given sequence, just base position. See my comment on the answer below for add ...
written 7.5 years ago by Blunders1.1k
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Comment: C: Consensus Sequence Algorithms And Notation
... @bilouweb: True, though using that algo, [AATGC], [A], [AAA], [AA-], etc. would all have the same result, right? Plus, what would [AAGG] be? There has to be a better way that condense info without losing info. Thinking something along the lines of relative probablity, entropy, etc. ...
written 7.5 years ago by Blunders1.1k
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Consensus Sequence Algorithms And Notation
... Trying to better understand methods of reaching a consensus sequence, while keeping the input as simple as possible. For example, say there are 10 bases numbered 0123456789, and each base listed within the brackets is the base pulled from the same base position. 0[GG-GGA-GA-TCT-AC] 1[GGAG-GTAAC-TC ...
consensus written 7.5 years ago by Blunders1.1k • updated 7.5 years ago by brentp22k
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In Perl, Method For Extracting Fileheaders From Affy Cel File.
... Looking for a Perl script to extract fileheaders from Affy CEL file. I've found Bioconductor's "Affymetrix File Parsing SDK" -- but trying to avoid installing yet another system into my pipeline. ...
perl affymetrix file parsing written 7.5 years ago by Blunders1.1k • updated 7.3 years ago by Nibua60
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Comment: C: Is It Possible To Find For A Given Gene The Coding Sequences On Ensembl?
... @Jorge Amigo: Thanks. Any idea what was "Sequence unavailable" might mean? Here's an example for ENSG00000139618 http://www.biomart.org/biomart/martview/dee22528d7a6005fe66e60b279c6dbe6 ...
written 7.6 years ago by Blunders1.1k
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Is It Possible To Find For A Given Gene The Coding Sequences On Ensembl?
... This information has been found on NCBI, but attempting to find it on Ensembl. On NCBI, is was found by: Going to this URL; clearly BRCA2 would have to be replaced if the search was for another gene. Clicking a related result On that page scroll down to "RefSeqs of Annotated Genomes" Within that ...
cds ensembl written 7.6 years ago by Blunders1.1k • updated 7.6 years ago by Bert Overduin3.6k

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