User: cocchi.e89

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cocchi.e8950
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Posts by cocchi.e89

<prev • 63 results • page 1 of 7 • next >
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covid-19 puclicly available data
... I don't even know if this is the best place to ask it but, as a bioinformatician community think somebody here may know something. I am wondering what kind of databases and data are actually available regarding covid-19 infection, especially epidemiological and clinical characteristics. Is there any ...
data covid clinical written 19 days ago by cocchi.e8950
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Comment: C: protein 3D model not showing all AA residues
... Thanks for the useful answer! Is there any way to model this part? ...
written 6 weeks ago by cocchi.e8950
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Comment: C: protein 3D model not showing all AA residues
... But they have a limitation to 1500 AA sequence. I suppose I cannot cut a portion of the protein and hoping that the results will be reliable, right? ...
written 6 weeks ago by cocchi.e8950
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protein 3D model not showing all AA residues
... Maybe is a silly question but I found no clear information about. I generated the 3D models of a COL4A5 protein with a missense mutation c.2546G>A p.(Gly849Glu) through [Phyre2][1] ([here link to my results][2]) and the protein inserted FASTA is ~1690 residues. The generated primary model is only ...
model protein mutation phyre2 written 6 weeks ago by cocchi.e8950 • updated 6 weeks ago by Mensur Dlakic4.3k
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retrieve AA sequence change from a frameshift mutation
... I am trying to visualize the effect of a particular frameshift mutation in COL4A5 gene of a patient (human) > NM_033380.1(COL4A5): c.2777del p.(Gly926Alafs*70) I know ([correct me if I'm wrong][1]) that this mutation causes a frameshift where the FIRST AA changed is the Glycin in position 926 ...
protein sequence visualization frameshift mutation written 6 weeks ago by cocchi.e8950 • updated 6 weeks ago by KevinL20
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merge VCF single variants G>A and C>A into GC>AA
... I am working with some WES human data, I am trying to replicate some results from previous study from which I have the HGVS.c variants annotation and I need to get the genomic coordinates. I am doing pretty good with VEP but I found a couple of variants that are delins of 2 bases and resulted in spl ...
vcf exome variants hgvs written 9 weeks ago by cocchi.e8950 • updated 9 weeks ago by GokalpC50
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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 9 months ago by cocchi.e8950 • updated 9 months ago by genomax80k
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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 9 months ago by cocchi.e8950
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Comment: C: protein domain "official" DB
... thank you very much @genomax ...
written 9 months ago by cocchi.e8950
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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 9 months ago by cocchi.e8950

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