User: Learner

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Learner 110
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Posts by Learner

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uniprot protein information about reactions
... I am interested in retrieving the information for proteins and understand which ones are enzyme and which ones are not. Is there an easy way to do it for a large number of genes ? using uniprot ? ...
gene written 7 hours ago by Learner 110
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Comment: C: extract information from Uniprot
... @Alex Reynolds I think there are many genes are assigned to one GO, do you think it is possible to do that before you do this ? ids <- unique(df$V4) ...
written 7 hours ago by Learner 110
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Comment: C: annotation - biomaRt - getBM - multiple entrez ID
... @Mike Smith I get this error but I don't know the argument of 'listFilters' Error in getBM(values = ex, filters = "go_id", mart = mart, attributes = c("go_id", : Invalid filters(s): go_id Please use the function 'listFilters' to get valid filter names ...
written 1 day ago by Learner 110
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Comment: C: annotation - biomaRt - getBM - multiple entrez ID
... @Kevin Blighe instead the gene_name, please now try this one, you will see that you get error ex <- c("GO:0000002","GO:0042254","GO:0042254","GO:0000022","GO:0000028","GO:0000028","GO:0000045") ...
written 2 days ago by Learner 110
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Comment: C: annotation - biomaRt - getBM - multiple entrez ID
... @Kevin Blighe Kevin, how did you check for it? I checked the attributes but with no success. is there a way to unique them based on GO id? ...
written 2 days ago by Learner 110
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Comment: C: How to retrieve sets of protein sequences?
... @vkkodali I found where the issue was. your solution is the best solution. I think if I want to extract the IDs from the fasta file, I can simple do the following right ? grep '^>' uniprot_seqs.fasta | cut -f2 -d '|' | sort ...
written 2 days ago by Learner 110
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annotation - biomaRt - getBM - multiple entrez ID
... Hi I am trying to follow what is said in here , however, without any success https://support.bioconductor.org/p/52407/ when I do it as described here, I am fine ex <- c("ENSG00000215417", "ENSG00000224078", "ENSG00000198366", "ENSG00000196176", "ENSG00000166012", "ENSG00000158406", ...
genome biomart entrez written 2 days ago by Learner 110 • updated 2 days ago by Emily_Ensembl16k
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Comment: C: How to retrieve sets of protein sequences?
... @vkkodali actually I am using Uniprot which is what I am interested in , however, it is killing me, for example check for these gene P21333 O43707 P68363 you see that they exist in Uniprot but when I use your approach , I get nothing. do you think the format of .txt would influence ? also is ther ...
written 2 days ago by Learner 110
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Comment: C: How to retrieve sets of protein sequences?
... @vkkodali how can I know which proteins sequences are downloaded and which ones are not? also should I install epost and efetch ? because it gives me an error ...
written 2 days ago by Learner 110
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How to retrieve sets of protein sequences?
... I have a set of protein accession number . I want to retrieve their sequences but programmically Is there anyway to do that from Uniprot. There is a page description on Uniprot itself but to be honest I could not understand it Any comment would be appreciated Thanks ...
gene written 3 days ago by Learner 110 • updated 3 days ago by vkkodali700

Latest awards to Learner

Popular Question 3 months ago, created a question with more than 1,000 views. For focus on specific pathway
Popular Question 5 months ago, created a question with more than 1,000 views. For focus on specific pathway
Popular Question 5 months ago, created a question with more than 1,000 views. For how to convert SwissProt or UniProt gene names to standard ID
Popular Question 5 months ago, created a question with more than 1,000 views. For focus on specific pathway
Popular Question 5 months ago, created a question with more than 1,000 views. For focus on specific pathway
Supporter 6 months ago, voted at least 25 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For how to convert SwissProt or UniProt gene names to standard ID
Centurion 2.1 years ago, created 100 posts.
Rising Star 2.5 years ago, created 50 posts within first three months of joining.

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