Tag: snap

LAMMPS Patch 24 March 2022 Release Overview What is LAMMPS used for? LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of…

In nature, microbes have evolved different systems to sense external stimuli. Synthetic biology approaches (1) repurpose these systems as biosensors to specifically and sensitively detect various targets of interest. Although various highly sensitive and specific laboratory-based analytical methods (including high-performance liquid chromatography and mass spectrometry) can detect small-molecule targets, they…

Associated RNAi Experiments Homology BLAST of peroxisomal multifunctional enzyme type 2-like vs. L. salmonis genes Match: EMLSAG00000010112 (supercontig:LSalAtl2s:LSalAtl2s668:190059:194758:1 gene:EMLSAG00000010112 transcript:EMLSAT00000010112 description:”augustus_masked-LSalAtl2s668-processed-gene-1.1″) HSP 1 Score: 102.064 bits (253), Expect = 2.195e-25Identity = 65/191 (34.03%), Postives = 101/191 (52.88%), Query Frame = 0 Query: 134 GKVALVTGAGGGLGKAYALLLASRGASVVVNDLGGSRTGEGQSSKAADEVVNEIRQKGGKAV—–GNYDSVEDGEAVIKTALDNFGRIDIVINNAGILRDRSIGRTSDSDWDLVQKVHLRGAFQVIRAAWPHMKKQKYGRIINTSSVAGIFGNFGQSNYSSAKAGLIGLTSTLAIEGERSGIQANVIVP 319 GKVAL+TGA G+G++ A+L A…

Every few months we highlight a subset of the new plasmids and viral preps in the repository through our hot plasmids articles. These articles provide brief summaries of recent plasmid deposits and we hope they’ll make it easier for you to find and use the plasmids you need. If you’d ever…

Computer Vision Researcher / Research Scientist – 12 month contract This is a unique opportunity to snap up very quickly. Our client is a leading technology firm looking to hire a recent graduate / post doc graduate. An ideal role for a newly qualified individual looking to gain experience within…

Moore, Stan Gerald. Kokkos and SNAP work in support of EXAALT and LAMMPS.. United States: N. p., 2020. Web. Moore, Stan Gerald. Kokkos and SNAP work in support of EXAALT and LAMMPS.. United States. …

We describe the engineering of a novel DNA-tethered T7 RNA polymerase to regulate in vitro transcription reactions. We discuss the steps for protein synthesis and characterization, validate proof-of-concept transcriptional regulation, and discuss its applications in molecular computing, diagnostics, and molecular information processing. We propose a method for regulating polymerase activity…

The workflow consists of growing cells in strictly controlled environmental conditions, rapidly chilling them using melting water/ice and fixing with pre-optimized concentration of formaldehyde and incubation time. The fixation reaction is then quenched using excess of primary amino group-containing compounds, such as glycine or tryps. Cells are collected, washed and…

Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…

Pancreatic duct infusion is an important technique that can allow for lineage tracing, gene introduction, and cell line-specific targeting. A pancreatic duct infusion technique for drug and viral delivery to pancreatic cells is presented here. The overall goal of this pancreatic duct infusion procedure is to enable lineage tracing, gene…

Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…

Ninety per cent of the bacterial genomes sequenced belong to a restricted set of only 20 bacterial species, out of an estimated 45,000*, highlighting the knowledge gaps in available genomic data and showing how this distorts our view of bacterial diversity, new research has suggested. In a new study, from…

The National Open API Payment Standard, abbreviated to SNAP, is the national open API payment standard published by Bank Indonesia to create a healthy, competitive and innovative payment system industry, while promoting integration, interconnectivity and interoperability as well as secure and reliable payment system infrastructure; and/or…

to grep pattern 1 I am interested to grep the line only containing the word “gene” present at column 3 of this following file but this word is also present at each line in column 9 of this file. Please any suggestion to use the grep in bash/linux and select…

After the article in Nature about the open-source of AlphaFold v2.0 on GitHub by DeepMind, many in the scientific and research community have wanted to try out DeepMind’s AlphaFold implementation firsthand. With compute resources through Amazon Elastic Compute Cloud (Amazon EC2) with Nvidia GPU, you can quickly get AlphaFold running…

Error in gff file 1 I am trying to use gff with bedtools intersect to get the reads count to the gene. However, it is throwing an error: Error: Invalid record in file “obtectus_HiC.gff”. Record is HiC_scaffold_1502 maker gene -246 584 . + . ID “maker-@000032F|arrow|arrow-snap-gene-3.48”; Name “maker-@000032F|arrow|arrow-snap-gene-3.48”; Any idea…

How to train annotations tools 1 I would like to train Augustus, SNAP and GlimmerHMM. I found protein sequences in GenBank and in orthodb.org. Furthermore, I found HMM files on busco-data.ezlab.org. $ wget -c busco-data.ezlab.org/v5/data/lineages/viridiplantae_odb10.2020-09-10.tar.gz $ wget -c v100.orthodb.org/download/odb10_plants_fasta.tar.gz Are there any instructions on how to train those annotations tools?…

Kaggle ARC challenge has set May 27 as the final submission deadline for the ARC challenge. Kaggle Datasets. The internet is a treasure trove of valuable information for aspiring data scientists. • updated 2 years ago (Version 3) Data Tasks Code (1,473) Discussion (1) Activity Metadata. (Some might need you…

Statistics and reproducibility For multiplex fluorescent in situ hybridization (FISH) and immunofluorescence staining experiments, each ISH probe combination was repeated with similar results on at least two separate individuals per species, and on at least two sections per individual. The experiments were not randomized and the investigators were not blinded…

12.01pm Holiday snap It turns out that Benjamin List was on holiday in Amsterdam when he got the call letting him know that his life was going to change forever (at least he was in a timezone amenable to getting the call, unlike David MacMillan, who’s based at Princeton University). …

A few months ago, I’d never heard of Oxford Nanopore (LSE:ONT). Yet after a successful IPO last week, the shares are now listed for unconditional trading for retail investors. From an IPO price of 425p, the Oxford Nanopore share price closed yesterday at 596p. This 40% jump at the start…

snap installation error 1 Hello everybody I want to annotate the genomes of fungi and I wanted to install snap, I already installed on ubuntu. now i’m working on debian, the installation stops that i did “make” i get an installation error below : root@debian:software/snap# make make gcc make[1] : on…

Short open reading frames (ORF) upstream of the canonical ORF (uORFs) are found in about 40% of human protein-coding transcripts (1⇓–3). uORF-containing genes were shown to participate in heavily regulated processes, including differentiation, cell cycle control, and stress responses (4⇓–6). Ribosome profiling data revealed that many uORFs are translated (3,…

phyloseq Handling and analysis of high-throughput microbiome census data. Detecting the periodontal pathogens at the subgingival plaque requires skilled professionals to collect samples. Import mothur list and group files and return an otu_table. In a randomized, double-blind, placebo-controlled trial, we assessed the effect of Lactobacillus reuteri supplementation, from birth to…

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…

I’ve always been a fan on Sandbox Games. GMod is no exception. I liked the idea of making your own games/levels using Source Engine assets without having to learn or use Source. In fact, I loved it so much, I decided to make my own version of GMod in DevSquare….

Significance Putatively ancient asexual species pose a challenge to theory because they appear to escape the predicted negative long-term consequences of asexuality. Although long-term asexuality is difficult to demonstrate, specific signatures of haplotype divergence, called the “Meselson effect,” are regarded as strong support for long-term asexuality. Here, we provide evidence…

With help from John Hendel and Leah Nylen — Agency agenda: The FTC plans to rescind Trump-era vertical merger guidelines at today’s open meeting. But how much will that really change? — Broadband moves: As House committees wrap up their portions of Democrats’ social spending package , some lawmakers are…

Rishi Sunak has given his blessing to a multibillion-pound trend that has seen foreign private equity firms snap up British businesses, describing the buying spree as “good news” for the economy. The chancellor was speaking at the launch of Treasury Connect, an event intended to bring together fast-growing tech businesses…

Associated RNAi Experiments Homology BLAST of probable dimethyladenosine transferase-like vs. L. salmonis genes Match: EMLSAG00000006273 (supercontig:LSalAtl2s:LSalAtl2s341:673186:674124:1 gene:EMLSAG00000006273 transcript:EMLSAT00000006273 description:”augustus_masked-LSalAtl2s341-processed-gene-6.3″) HSP 1 Score: 484.567 bits (1246), Expect = 2.083e-174Identity = 227/310 (73.23%), Postives = 259/310 (83.55%), Query Frame = 0 Query: 9 KVRKTGSGMSTVEAAGSGGGGQQGMVFNTGLGQHILKNPLVVQSIIDKAALRSTDVVLEIGPGTGNLTVRALEKCKKLIACEVDPRMVAELQKRVQGTHFQSKLQIMVGDVIKTDLPFFDACVANVPYQISSPLVFKLLLHRPFFRCAVLMFQREFAQRLVAKPGDKLYCRLSINTQLLARVDHVMKVGKGNFRPPPKVESSVVRIEPRNPPPPINFKEWDGLTRVAFVRKNKTLGAAFNQTTVLMMLEKNYRVHLSLADEPVPEKIDIKSIIETVLAEIAFKEKRARSMDIDDFMKLLHAFNAKGIHFV 318 KV+ T + GG+QG+VFNT LGQHILKNP VV…

COVID-19 laboratory screening Nasopharyngeal/Nasal/Oropharyngeal swabs in viral transport medium (VTM) received from acute phase patients with defined symptoms, asymptomatic cases with contact history with positive patients/ travel history were processed for laboratory confirmation of SARS-CoV-2 at Defence Research and Development Establishment, (DRDE) Gwalior, M.P., India. These samples were referred for…

Less and less genes predicted with each iteration of SNAP/MAKER 0 Hi I am annotating a de novo genome using MAKER. I first ran maker with est and protein information from a closely related species, with est2genome and protein2genome on. I then ran MAKER with SNAP switched on, using the…

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problem with Trinity command run in denovo transcriptome assembly 0 I tried to run my Trinity command for the assembly but this is the error I’ve been getting .. please help let me know where did I go wrong. I’m new to this analysis field. Error, cannot locate Trinity-specific tool:…

problem in trinity installation 0 I am using ubunto 16.4 I tried to install trinity by following the instructions on the web. After downloading and extracting, I typed “make” the “make plugins” Then I ran trinity on test data as mentioned i.e byu typing “./runMe.sh” but following error is shown:…

I am trying to do a second round of maker genome annotation with ab initio prediction by snap. The error I am getting is as follows: error: unknown command “genome.hmm”, see ‘snap help’. ERROR: Snap failed –> rank=NA, hostname=bioinformatics ERROR: Failed while preparing ab-inits ERROR: Chunk failed at level:0, tier_type:2…