User: damianosmel
damianosmel • 0
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Posts by damianosmel
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... 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 ...
written 7 days ago by
damianosmel • 0
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... 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
damianosmel • 0
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... 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 ...
written 17 days ago by
damianosmel • 0
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... 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
damianosmel • 0
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... 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)
...
written 3 months ago by
damianosmel • 0
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