User: damianosmel

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Posts by damianosmel

<prev • 5 results • page 1 of 1 • next >
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Retrieving similarity of Interpro domains
... Dear all, I would like to ask for meta-data to assess similarity of Interpro domains. I have checked the ParentChildTreeFile.txt, the type description (repeat,domain,etc) (file: entry.list.tsv) and the gene ontology annotation (GO) for each domain. However I am not sure if this metadata are enough ...
interpro meta-data written 7 days ago by damianosmel0
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Answer: A: Automatically retrieving interpro domain information ( to combine with phylogent
... Hi Venurah, By my little experience with Interpro database. You can retrieve for each interpro id the connecting database ids (for example PFAM, CDD, etc). Then you can check each connecting database if it contains the domain profile (multiple sequence alignment (MSA)). Then you can build the phylo ...
written 7 days ago by damianosmel0
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Does ParentChildTreeFile.txt of Interpro has a specific tree format?
... Hey all, I want to parse the ParentChildTreeFile of interpro database, found at: https://www.ebi.ac.uk/interpro/beta/download/ I would like to use Python to parse it. However after reading the user_manual from interpro, I couldn't find any details for the format of the file. Does the file follow ...
interpro tree_format parentchild written 17 days ago by damianosmel0
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Comment: C: snpEFF chr not found error bacterial genome
... Hi SemiQuant, thank you for your answer! Today I have encountered the same problem. I could find your answer in SnpEff documentation: http://snpeff.sourceforge.net/SnpEff_faq.html Damianos ...
written 3 months ago by damianosmel0
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Calculate the SNP effect on binding site and RNA fold for Bacteria
... Dear all, I would like to recalculate the effect of SNPs for the RNA fold and the binding site for bacteria genomes. I have the vcf file with SNPs comparing the isolates to the reference genome. For the effect of SNP on RNA fold I have found: - rnascan (https://github.com/morrislab/rnascan) ...
bacteria rna_fold binding_site snp written 3 months ago by damianosmel0

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