User: Morgan Howard

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Posts by Morgan Howard

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Iterate through sever annotation database packages
... Hello, I am looking for a method in R to check a list of accession numbers against annotation databases for 19 species. In theory the code below should extract the ENTREZID, SYMBOL, GENENAME and match the mapped results with the results file via the ACCNUM mapped <- foreach(i = dbMap$dbName ...
annotation R written 8 months ago by Morgan Howard0 • updated 8 months ago by James W. MacDonald51k
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Comment: C: Matching GenBank Accession Number with corresponding Biomart results
... Thank you immensely, this is a perfect solution to my issue. I am not expecting all accessions to have a hit. This option also is able to be widened to other species with the other databases available. ...
written 8 months ago by Morgan Howard0
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Comment: C: Matching GenBank Accession Number with corresponding Biomart results
... So if I am understanding you correctly, one of the attributes would be need to the accession number which the ensembl biomart database does not support. If you take the first result from my results file and enter it into both EMBL-EBI and the NCBI databases, the information is identical. I assume t ...
written 9 months ago by Morgan Howard0
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Matching GenBank Accession Number with corresponding Biomart results
... Hello, I am taking a large list of accession numbers from NCBI’s EST and GenBank databases and using biomart R package to query the the Ensembl mart and the human gene Ensembl dataset in order to retrieve the attributes entrezgene_trans_name, entrezgene, description, and transcript_biotype. This al ...
annotation biomart R written 9 months ago by Morgan Howard0 • updated 9 months ago by James W. MacDonald51k

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