User: cocchi.e89

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cocchi.e8930
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Posts by cocchi.e89

<prev • 57 results • page 1 of 6 • next >
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protein domain start-stop codons database
... I'm working on some variations (exome, human) and I got their domain feature with VEP. e.g. of a result: `Pfam_domain:PF01762&hmmpanther:PTHR11214&hmmpanther:PTHR11214:SF28&Low_complexity_(Seg):seg` I need to get back from this domain to its codons coordinates (e.g. PANTHER `PTHR1121 ...
domain codon vep database written 4 months ago by cocchi.e8930 • updated 4 months ago by genomax74k
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Comment: C: Get genomic coordinates for protein domain
... And there is an available database to have the start&stop codons of each PANTHER domain? Instead of manually searching it every time? ...
written 4 months ago by cocchi.e8930
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Comment: C: protein domain "official" DB
... thank you very much @genomax ...
written 4 months ago by cocchi.e8930
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Comment: C: protein domain "official" DB
... I know, but I'd like to know if there's a more maintained, widely used etc. Maybe there's not ...
written 4 months ago by cocchi.e8930
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protein domain "official" DB
... I'm working on some variants (exome, human) and I found the different outputs printed for each domain by VEP, e.g. : ex. VAR `1-949422-G-A` : `Gene3D:3.10.20.90&Pfam_domain:PF00240&PROSITE_profiles:PS50053&hmmpanther:PTHR10666&hmmpanther:PTHR10666:SF81&SMART_domains:SM00213&S ...
vep variation protein human domains written 4 months ago by cocchi.e8930
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Comment: C: uniprot variant classification DB retireve
... that's great! Thank you very much @elisabethgasteiger ...
written 4 months ago by cocchi.e8930
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Comment: C: how can a DELETION be not a NULL variant?
... In the ACMG classification, PVS1 explanation: "Not a null variant." ...
written 4 months ago by cocchi.e8930
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how can a DELETION be not a NULL variant?
... I've found a var (exam, human) in ROBO2 gene: `3-77684075-ACAG-A` According to [Varsome][1] this is not a NULL variant. Sorry if it sounds silly, but how can a DELETION not being a NULL variant? Thanks a lot in advance for any help! [1]: https://varsome.com/variant/hg19/3-77684075-ACAG-A ...
exome indel deletion variant acmg written 4 months ago by cocchi.e8930 • updated 4 months ago by Jean-Karim Heriche21k
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uniprot variant classification DB retireve
... I'm working on some variants (exome, human) annotation. I'd like to retrieve the UNIPROT info about the variant (e.g. "disease" when known as disease causing variant etc). How can I do that? I tried with `--uniprot` VEP command but it only output the var uniprot transcript. Thanks a lot in advance ...
variant vep uniprot ensembl written 4 months ago by cocchi.e8930 • updated 4 months ago by Elisabeth Gasteiger1.7k
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Comment: C: Retrieve base position/coordinates due to AA position on a protein
... Thank you very much Pierre. Have a look at my comment to your reply there: https://www.biostars.org/p/280271/#384092 ...
written 5 months ago by cocchi.e8930

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