Tag: VG

Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps

Genomic features of two Anastatus wasps, A. japonicus and A. fulloi We employed PacBio high-fidelity (HiFi) long-read sequencing and Illumina short-read sequencing technologies to generate high-quality contigs for two Anastatus wasps, A. japonicus and A. fulloi (Supplementary Tables 1 and 2). These contigs were further scaffolded using Hi-C libraries to…

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MSPCD: predicting circRNA-disease associations via integrating multi-source data and hierarchical neural network | BMC Bioinformatics

Problem description Limited by time and cost, exploring the correlations between circRNAs and human diseases based on biological experiments has encountered many difficulties and bottlenecks. Instead of traditional experiments, computational methods are proved to be an efficient and accurate way to discover the potential connections between circRNAs and diseases. Data…

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Nanobody-based RFP-dependent Cre recombinase for selective anterograde tracing in RFP-expressing transgenic animals

Screening of efficient mCherry-binding protein (MBP) pairs to design Cre recombinase dependent on RFPs First, we aimed to construct Cre recombinase dependent on RFPs based on the reported tool named Cre-DOG30. In this system, N-terminal and C-terminal split Cre recombinase fragments are fused with specific nanobodies for target proteins, and…

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Causes of ocular inflammation linked to AAV gene therapy

Low-grade inflammation seems to be associated with baseline disease in inherited retinal dystrophies (IRDs), according to Christine N. Kay, MD, a surgeon at Vitreoretinal Associates, in Gainesville, Florida. Examples of XX include zonular instability in cataract surgeries resulting in intraocular lens dislocations in retinitis pigmentosa (RP), presence of anterior vitreous…

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Environmental Factor – May 2022: Scientific moonshot: Now is the time to sequence RNA, expert says

Rick Woychik, Ph.D., directs NIEHS and the National Toxicology Program. (Image courtesy of NIEHS) Almost two decades have passed since the first sequence of a complete set of DNA was released as part of the Human Genome Project. That initiative expanded understanding of certain cancers, boosted the effectiveness of some…

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On a reference pan-genome model (Part II)

12 July 2019 I wrote a blog post on a potential reference pan-genome model. I had more thoughts in my mind. I didn’t write about them because they are immature. Nonetheless, a few readers raised questions related to my immature thoughts, so I decide to add this “Part II” as…

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hypothetical protein DAPPUDRAFT_213302, maker-scaffold2255_size18018-snap-gene-0.6 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of hypothetical protein DAPPUDRAFT_213302 vs. L. salmonis genes Match: EMLSAG00000000401 (supercontig:LSalAtl2s:LSalAtl2s1063:86108:87342:-1 gene:EMLSAG00000000401 transcript:EMLSAT00000000401 description:”maker-LSalAtl2s1063-snap-gene-0.46″) HSP 1 Score: 149.443 bits (376), Expect = 4.121e-44Identity = 91/196 (46.43%), Postives = 119/196 (60.71%), Query Frame = 0 Query: 14 MDKITDLQVEPLT–NSRFVKPLRLRFKQDGKVKVWDLIQCHASVAVVIFNQTTQKFVFVRQFRPAVYFSALRRAQGDVEPGTQFKGDEIDPKVGITLELCAGIVD-KSKSLIEIAHEEILEETGYDVPMNLIEEIQTFPVGVGVGGENMTLFCAEVTEAMRKGPGGGLAEEGEMIDVIEMGVEETRTLMRAKSVT 206 MDK+ VEPL +SRFV P R+ ++Q+G…

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Merging .gam files

Merging .gam files 1 Can anyone point me towards a method to merge gam files that are created by using ‘ vg map ‘ to map illumina reads to my genome graph? I would like to be able to map all of the sequencing runs separately and then merge the…

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Creating a variation graph for Giraffe alignment from assemblies

Creating a variation graph for Giraffe alignment from assemblies 0 I have a collection of ~100 4.5 megabase haploid assemblies that I would like to map to using giraffe. However, I am not completely clear on what the best practices are to construct the graph starting from the assemblies. I…

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