User: krc3004

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krc30040
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Posts by krc3004

<prev • 7 results • page 1 of 1 • next >
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Obtaining MHC peptide binding groove protein sequences
... Hi all, I am trying to obtain the protein sequences of the peptide binding grooves of MHC class I and class II alleles, but am unsure how to go about it. We know that for class I, the peptide binding groove is exons 2 and 3, and for class II the binding groove is exon 2, but I'm not sure how to ex ...
mhc ensembl imgt hla sequence written 1 day ago by krc30040
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dN/dS within and between species
... Hi all, Recently I have been very interested in calculating the dN/dS ratio to estimate rates of nonsynonymous and synonymous substitutions. Since I've just started learning the theory, I have a few basic questions (apologies if any of these are stupid!). Thanks for your help! - One of the appli ...
phylogeny hyphy mega paml msa written 7 weeks ago by krc30040
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Comment: C: Using ape package in R to pull genbank sequences
... Thank you Kevin! This solution works on my end but it is indeed messy, as you suggest...not sure why the ape package is returning the incorrect sequence. A further question is how to obtain the nucleotide sequence for these accessions but perhaps I can work that out separately...thanks again! ...
written 10 weeks ago by krc30040
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Comment: C: Using ape package in R to pull genbank sequences
... genomax, thanks very much for your help- I will try this. Is there any way to use efetch to get the nucleotide sequence as well? ...
written 10 weeks ago by krc30040
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Using ape package in R to pull genbank sequences
... Hi all- I am trying use the ape package in R to pull protein sequences from GenBank. The sequence I'd like to retrieve is the following: https://www.ncbi.nlm.nih.gov/protein/AAG26087.1 To do this I used the following code: library(ape) kl_seq = read.GenBank("AAG26087.1", as.character = T ...
ncbi R genbank ape written 10 weeks ago by krc30040 • updated 10 weeks ago by Kevin Blighe24k
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Converting TCGA/GDC IDs
... Hi all, I'm using GDC to bulk download RNA-seq data from TCGA. I'm able to download data just fine, but the filenames are the UUIDs, as shown below: https://portal.gdc.cancer.gov/files/c85a6f34-7b6b-4677-beac-44f06bcc5c32 What I really want are the Entity IDs, also in the above link. Is there a ...
tcga gdc rna-seq written 9 months ago by krc30040
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How to Interpret COSMIC/HGVS Gene Fusion Format
... Hi all, I'm trying to analyze gene fusion data from COSMIC and am having difficulty interpreting the HGVS format/documentation. Here is documentation from COSMIC: http://cancer.sanger.ac.uk/cosmic/help/fusion/summary and here is documentation from HGVS: http://www.hgvs.org/mutnomen/recs-RNA.h ...
hgvs cosmic fusion translocation written 11 months ago by krc30040

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