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... The way I see it, you have to download the bundle with all sequencing files again. If you want to get the "RELEASE.metalink" file that contains the information on the *fasta.gz files from an older version, e.g. "2019_03": ftp://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2019_03 ...
written 8 weeks ago by daniel.magnus.bader30
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... Hello Herve, Sorry for sleeping so long. I am just at the next update cycle right now. I wrote my own file parser and do not use Biostrings at the moment, but I did not check the sanity of the download again. Uniprot offers this solution for download sanity: https://www.uniprot.org/help/metalin ...
written 8 weeks ago by daniel.magnus.bader30
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... Dear all, I am creating a local organism-specific version of uniproton on our server. Using the Bioconductor Biostrings package I experienced an "embedded nul string" error with the readAAStringSet() function, but only on the trembl download, not for the swissprot fasta file. **Q1: Can you ...
written 5 months ago by daniel.magnus.bader30
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... Thanks. Looks like the perfect fit! ...
written 9 months ago by daniel.magnus.bader30
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... Thanks to the suggestions from Michael Lawrence and Herve Pages, I guess it should work as follows: 1. Identify all coding SNVs, e.g. via VariantAnnotation::predictCoding() 1. Injecting coding SNVs into the genome, e.g. via BSgenome::injectSNPs() 1. Concatenate the exons per protein isoform of ...
written 9 months ago by daniel.magnus.bader30
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... Thanks Herve, However, I think injectSNPs should be sufficient, since I start from genome coordinates in a VCF. Best, Daniel ...
written 9 months ago by daniel.magnus.bader30
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... Thanks for the reply sheperl. I did not want to start right away with an issue, but now I posted it here: https://github.com/Bioconductor/VariantAnnotation/issues/24 Meanwhile, I will look at BSgenome::injectSNPs() which sounds indeed very interesting. Thanks Michael! ...
written 9 months ago by daniel.magnus.bader30
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... Dear all, I am investigating the proteome of human cancer samples and want to insert their genetic variations into the reference proteome fasta sequences to increase the sensitivity of my peptide/protein quantification. **Can you implement this "proteomeVariantInsertion()" in the VariantAnnotation ...
written 9 months ago by daniel.magnus.bader30