Tag: sv

Issue Title State Comments Created Date Updated Date Mapping reads against multi references. Any proposition? open 0 2022-06-28 2022-06-30 Inversion between tandem repeats yields misalignment closed 1 2022-06-21 2022-06-30 use minimap2 to extract mitochondrial reads from genome assembly open 0 2022-06-20 2022-06-30 Asking for #301 to be reopened closed 0…

The heat-shock response is represented by a small set of genes in C. elegans We initially aimed at identifying those HSE-containing promoters that are most strongly upregulated under heat-stress conditions. Given that the HSR is complex in nematodes we used data from several heat-shock studies based on microarray and RNAseq…

A special issue of Non-Coding RNA (ISSN 2311-553X). Deadline for manuscript submissions: 30 November 2022 | Viewed by 9 Special Issue Editors Dr. Mirolyuba Ilieva E-Mail Website Guest Editor Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen SV, DenmarkInterests: non-coding RNAs; stem cell biology; neuroscience Special…

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Yale Cancer Center (YCC) will hold its Fifth Annual Trainee Colloquium virtually on Friday, June 10, 2022 from 8:30am – 1:15pm. This will be a forum for Yale trainees to highlight their research, exchange ideas, and initiate collaborations. We invite predoctoral MD, PhD, MD-PhD students, postdoctoral associates, postdoctoral fellows, residents,…

Benchmark dataset The following datasets, HomFam and OXFam were used as benchamrk datasets in “Application of the MAFFT sequence alignment program to large data – reexamination of the usefulness of chained guide trees”. HomFam This HomFam dataset is modified version of original HomFam dataset constructed by the authors of Clustal…

Volume 5 • Issue 3 • 1000132 J Pharmacogenomics Pharmacoproteomics ISSN: 2153-0645 JPP, an open access journal Research Article Open Access Prasanthi et al., J Pharmacogenomics Pharmacoproteomics 2014, 5:3 DOI: 10.4172/2153-0645.1000132 Research Article Open Access Pharmacogenomics Study of Clopidogrel by RFLP based Genotyping of CYP2C19 in Cardiovascular Disease Patients in…

Hello, I am looking to create a subset FASTA file from an existing FASTA file. The subset file should only include entries with certain accession numbers. I have created a BioIndexed File with the correct number of entries, but I am unsure how to use the getsubset function in this…

Sequencing data We used publicly available sequencing data from the GIAB consortium45, 1000 Genomes Project high-coverage data46 and Human Genome Structural Variation Consortium (HGSVC)4. All datasets include only samples consented for public dissemination of the full genomes. Statistics and reproducibility For generating the assemblies, we used all 14 samples for…

Stölting KN, Wilson AB. Male pregnancy in seahorses and pipefish: beyond the mammalian model. Bioessays. 2007;29:884–96. PubMed  Google Scholar  Whittington CM, Friesen CR. The evolution and physiology of male pregnancy in syngnathid fishes. Biol Rev Camb Philos Soc. 2020;95:1252–72. PubMed  Google Scholar  Rosenqvist G, Berglund A. Sexual signals and mating…

Job Description Bioinformatics Application Scientist (Actual title will depend on qualification and experience, including director level appointment) The Company: Universal Sequencing Technology Corporation (universalsequencing.com), a leading NGS biotechnology company engaged in long range/long read sequencing technology is relocating its headquarters from the greater Boston area to Carlsbad, CA where R&D…

Structural Variants (SV) Manta output interpretation: MantaBND and translocation lenght 1 Hi everyone, Manta novice here. Does anybody know how is possible to retrieve the translocation lenght from Manta SV output (if it makes sense)? For example, we have the following translocation: chr1 – chr6 : chr1 95016699 ]chr6:158767194]A MantaBND:4649:0:1:0:0:0:1…

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…

New York, USA – February 23, 2022 – The Bioinformatics-analysis division is a new division of CD Genomics that provides reliable next-generation and third-generation high-throughput sequencing data analysis, comprehensive technology services, database construction, and other related data analysis services. CD Genomics recently launched various types of genotyping analysis services, including…

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Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

Rare genetic disorders are caused by variants in major functional genes. Most are SNV or INDEL variants, but SVs, such as CNVs or chromosomal variants, can also be the cause. Recently, a large-scale study has also been published showing that CNVs were identified in 11-12% more infants and children with…

1. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985;82(20):6955–9. PubMed  PubMed Central  CAS  Google Scholar  2. Vos M, Quince C, Pijl AS, de Hollander M, Kowalchuk GA. A…

When I use ngmlr the sniffles worked. The coverage it more than 90% The code I sent on the github is exactly what it generated, I don’t think there any error Xu Zhang PhD Postdoctoral Associate, Department of Microbiology and Immunology Weill Cornell Medicine 1300 York Avenue, Box 62 New…

Position SummaryThis position is within Harman Automotive Division, located in Bangalore, India. In this position you work within a global engineering team and contribute to the design and development of the Harman Augmented Reality software product. The ideal candidate will have good analytical skills, knowledge of engineering discipline, and experience…

A Career at HARMANAs a technology leader that is rapidly on the move, HARMAN is filled with people who are focused on making life better. Innovation, inclusivity and teamwork are a part of our DNA. When you add that to the challenges we take on and solve together, you’ll discover…

Entry EC 2.3.1.68                 Enzyme                                  Name glutamine N-acyltransferase Class Transferases;Acyltransferases;Transferring groups other than aminoacyl groupsBRITE hierarchy Sysname acyl-CoA:L-glutamine N-acyltransferase Reaction(IUBMB) acyl-CoA + L-glutamine = CoA + N-acyl-L-glutamine [RN:R00577] Reaction(KEGG) R00577 Reaction Substrate acyl-CoA [CPD:C00040]; L-glutamine [CPD:C00064] Product CoA [CPD:C00010]; N-acyl-L-glutamine [CPD:C02716] Comment Phenylacetyl-CoA and (indol-3-yl)acetyl-CoA, but not benzoyl-CoA, can act as acyl donors….

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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…

Intensity of magnade’s attraction to a hunter. Learn how your comment data is processed. Find key bound to specified command string. Insomnia65 August 12, 2019 – TF2 Team. if you find this, don’t go around enabling it and then complaining about issues. The “size in K” is the block size…

Your message dated Sat, 18 Sep 2021 15:37:04 +0000 with message-id <e1mrcom-0000pb…@fasolo.debian.org> and subject line Bug#994290: fixed in gromacs 2021.3-3 has caused the Debian Bug report #994290, regarding gromacs build-depends on gcc-9 to be marked as done. This means that you claim that the problem has been dealt with. If…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Sat, 18 Sep 2021 08:17:59 -0700 Source: gromacs Architecture: source Version: 2021.3-3 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de…@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr…@debian.org> Closes: 994290 Changes: gromacs (2021.3-3) unstable; urgency=medium . * With GCC 10.3 in testing for all release…

compare SV results across samples – Manta, Delly 3 Hi folks, I have Delly and Manta results for a cohort of WGS tumour libraries. Some of the libraries are derived from the same sources using different methods in the lab and I want to be able to compare/contrast the sets…

Annotate Structural variants with population specific allele frequency values 0 Hi, Has anyone tried filtering structural variants based on pupulation specific allele frequency (AF) values (for example gnomAD-SV or phase 3 1000 genome SV)? I have a set of SVs that I detected using a multipronged approach. For prioritising variants,…

I’ve let the server stay open so you can join it and test for yourself. Game Garry’s Mod. It’s just textures (and maps, if you need it) for use as an addon to Garry’s Mod. From hunting down everyday objects in Prop Hunt to strangling and trampling pigs in Open…

1. Hackstein JH, Stumm CK. Methane production in terrestrial arthropods. Proc Natl Acad Sci USA. 1994;91:5441–5. CAS  PubMed  PubMed Central  Article  Google Scholar  2. Hackstein JHP, van Alen TA. Fecal methanogens and vertebrate evolution. Evolution. 1996;50:559–72. PubMed  Article  PubMed Central  Google Scholar  3. Borrel G, McCann A, Deane J, Neto…

It holds a 15% stake in the company and has valued its holding at £340m, giving a valuation of more than £2bn for the company. . While the company’s current shareholders have recorded its value at just over £2bn, analysts . Essay from the year 2011 in the subject Business…

This article was originally published here Comput Struct Biotechnol J. 2021 Aug 10;19:4435-4446. doi: 10.1016/j.csbj.2021.08.007. eCollection 2021. ABSTRACT Poly (ADPribose) polymerase inhibitors (PARPis) are clinically approved drugs designed according to the concept of synthetic lethality (SL) interaction. It is crucial to expand the scale of patients who can benefit from…

comparing variants between two VCF files 1 I have two VCF files (e.g. SV1.vcf.gz, SV2.vcf.gz) and a bed file (reg.bed). I would like to compare the variants among them in the BED regions. The comparison includes the common variants and unique variants present in SV1 and SV2. I am currently…

Tool:GRIDSS: the Genomic Rearrangement IDentification Software Suite 0 GRIDSS is typically used for detecting structural variation breakpoints from short read sequencing data but is a modular software suite containing a number of tools useful for the detection of genomic rearrangements including: A structural variant caller. The GRIDSS caller uses break-end…

Calculate the fraction of genome that is feature X 2 I am trying to calculate enrichment of Structural variant breakpoints and SNV locations in genomic features (exon, intron, 5’UTR…) in a non-human genome. To know whether a feature is over/underrepresented in a SV/SNV dataset, I first need to know the…

Interpretation of .gfa 1 I love .gfa, but sometimes I have trouble to understand them. I have used Flye with pacBio reads with defaults options to make a first shot at assemble a linear bacterial genome. The genome probably contains some plasmids or some phages sequences. Flye gave me the…

I’ve been trying to delve into the data from whole genome sequencing, specifically by looking at the already existing data in the 1000 genome project and gnomad, and I have a lot of questions. Does gnomAD contain the 1000gp samples? I’ve found many vcf including these: ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/hd_genotype_chip/ ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/integrated_sv_map/ ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/ gnomad.broadinstitute.org/downloads…

Karyotyping variation by ethnicity 0 Does the human karyotype vary based on ethnicity? If yes, then do clinical investigations of genetic abnormalities via karyotying need to be adjusted for such variations? If yes, how is this adjustment performed – some software I assume? If not, then why not? I was…