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User: Damianos P. Melidis

gravatar for Damianos P. Melidis
Reputation:
20
Status:
New User
Location:
Germany/Hannover/Leibniz University Hannover
Website:
https://damianosmel.gi...
Twitter:
damianosmel
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Google Scholar Page
Last seen:
16 hours ago
Joined:
1 year, 4 months ago
Email:
d**********@gmail.com

Passionate bioinformatician from sunny Athens!

Posts by Damianos P. Melidis

<prev • 11 results • page 1 of 2 • next >
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Comment: C: How to use entrezpy and Biopython Entrez libraries to access ClinVar data from
... Thank you for your reply. I see so I will need to think which of the two libraries to use. overlapping uids) yes the entrezpy library keeps all fetched uids in history, so I need to always keep the new ones. My concern was on when that list will become too long. entrezpy submodule, I use the esear ...
written 2 days ago by Damianos P. Melidis • 20
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Comment: C: How to use entrezpy and Biopython Entrez libraries to access ClinVar data from
... Thank you for the help. So I combine them as Entrezpy is developed by (mostly) one person compared to Biopython that is a community project, so the development is much more stable. And so I would prefer to use tools that will continue to develop. With this being said, I could not find any other way ...
written 5 days ago by Damianos P. Melidis • 20
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Comment: C: How to use entrezpy and Biopython Entrez libraries to access ClinVar data from
... Yes, before three days I posted also in stackoverflow in hope to get as much input/feedback as I could. ...
written 5 days ago by Damianos P. Melidis • 20
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How to use entrezpy and Biopython Entrez libraries to access ClinVar data from genomic position of variant
... For one of my projects of my PhD, I would like to access all variants, found in ClinVar db, that are in the same genomic position as the variant in each row of the input GSVar file. The language constraint is Python. Up to now I have used entrezpy module: entrezpy.esearch.esearcher. Please see more ...
python3 entrezpy clinvar biopython entrez written 4 weeks ago by Damianos P. Melidis • 20
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Comment: C: How to select pairs to have a significant sample for similarity
... Because I am working on a similarity function and I want to test how much this function correlates with the GO similarity. So I can't really make it with a little number of pairs of genes because then it would not be significant.. ...
written 9 months ago by Damianos P. Melidis • 20
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How to select pairs to have a significant sample for similarity
... Dear all, I have a list of biological entities (say genes) and I would like to compute all unique pairs (e.g (A,B,C)-> (A,B), (A,C), (BC)) and then calculate their similarity based on their GO. Good up to now, but the number of entities is say 2000 so the number of unique pairs is millions (2000 ...
similarity sampling pairs gene ontology written 9 months ago by Damianos P. Melidis • 20 • updated 8 months ago by Biostar ♦♦ 20
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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 10 months ago by Damianos P. Melidis • 20
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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 10 months ago by Damianos P. Melidis • 20
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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 11 months ago by Damianos P. Melidis • 20 • updated 10 months ago by Biostar ♦♦ 20
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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 13 months ago by Damianos P. Melidis • 20

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