Tag: OMA

The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

FAO, ITPS, GSBI, CBD & EC. State of knowledge of soil biodiversity – Status, challenges and potentialities, Report 2020. (FAO). doi.org/10.4060/cb1928en. 2020. Potapov, A. M. et al. Feeding habits and multifunctional classification of soil-associated consumers from protists to vertebrates. Biol. Rev. 97, 1057–1117 (2022). Article  PubMed  Google Scholar  García-Palacios, P.,…

Continue Reading The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

IPLOOK Unveils Visionary Product Roadmap for the Future of Core Networks

HONG KONG, Nov. 24, 2023 /PRNewswire/ — IPLOOK Networks, a global vendor of mobile core networks, recently revealed its latest product roadmap, highlighting strategic initiatives and upcoming feature releases. 2023 R6.7: TSN Release  R17 Feature Compliance V2X Trial 5GC+AI Advanced Research Space-Integrated-Ground Network Core Adaptation to Cloud Platform VMware Cloud…

Continue Reading IPLOOK Unveils Visionary Product Roadmap for the Future of Core Networks

RPA biosensors for rapid zoonoses screening

Introduction Since the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in 2019, this coronavirus has spread to more than 200 countries, cumulatively infecting 672 million people and causing 6.84 million deaths. Moreover, the emergence of numerous variant strains (α, β, γ, δ, and Omicron) presents a serious challenge for…

Continue Reading RPA biosensors for rapid zoonoses screening

Eva Kuusk – koolitused

Eva Kuusk teraapiate ja õpitubade aluseks on käsitlus terviklikust inimesest. Eesmärgiks on inimeste toetamine nende arengus, oma terviklikkuse tunnetamine ja teadvustamine, mille abil suurendada inimese isiklikku toimetulekut ning leida tema vajadusi arvestavad lahendused. Üksnes läbi selle saavad hakata meieni jõudma lahendused probleemidele ja kasvama elukvaliteet. Väljakutsed ja kriisid äratavad meis oskused…

Continue Reading Eva Kuusk – koolitused

Answer: OMA in AWS cloud

Hi, you can use [AWS Batch][1] to execute OMA. You can use [AWS Batch Array Jobs][2] for parallelization and use [Amazon EFS as filesystem][3]. You can also use [Amazon FSx for Lustre][4] if you need higher filesystem performance. You can avoid [throttling of Docker Hub image][5] pulls by using [Amazon…

Continue Reading Answer: OMA in AWS cloud

Researchers study how cells adapt to stressful and complex environments

Imagine the life of a yeast cell, floating around the kitchen in a spore that eventually lands on a bowl of grapes. Life is good: food for days, at least until someone notices the rotting fruit and throws them out. But then the sun shines through a window, the section…

Continue Reading Researchers study how cells adapt to stressful and complex environments

Maven Central: com.github.telecomsdn.openapi.sdk:oma:1.0.8-SR1%3Fsmo%3Dtrue

| Maven Central Repository No Results Found API DocHelpBrowseSign In 1.0.8-SR1%3Fsmo%3Dtrue Used in Loading… components pkg:maven/com.github.telecomsdn.openapi.sdk/oma@1.0.8-SR1%3Fsmo%3Dtrue Overview Overview Versions Versions Dependents Dependents Dependencies Dependencies Loading… Loading… Loading… Loading… Loading… Company Products Copyright 2023 Search Browse Publish Namespace Support API Documents Getting Started Help Validate Privacy Policy Terms of Service Log…

Continue Reading Maven Central: com.github.telecomsdn.openapi.sdk:oma:1.0.8-SR1%3Fsmo%3Dtrue

OMA in AWS cloud

OMA in AWS cloud 2 Dear colleagues, I am new in cloud environment and I would like to run OMA standalone in AWS environment. Firstly I would like to know if it is possible. Secondly, if it is, what are the parameters to use (AWS configuration specialy for all versus…

Continue Reading OMA in AWS cloud

Phylogenomics reveals the history of host use in mosquitoes

Taxon sampling and specimen collection All samples were collected legally following local requirements and our research complies with all relevant ethical regulations. Insect specimens were received at NC State University’s Insect Museum, pursuant to CITES permit 08US827653 (GRSCICOLL URI: grbio.org/cool/ij62-iybb). Our dataset contains representatives of 268 species from nine tribes,…

Continue Reading Phylogenomics reveals the history of host use in mosquitoes

Retrieving Chromosome Accession for Specific Gene Using Ensembl REST API

Hello! I have a list of gene IDs obtained from multiple sources via the OMA API. My goal is to download the gene sequences along with their genomic context. To achieve this, I need to acquire the accession numbers and coordinates of the assemblies in which they are annotated. I…

Continue Reading Retrieving Chromosome Accession for Specific Gene Using Ensembl REST API

Downloading Microsyntenic Fasta Sequences with Varying Chromosome Formats

Downloading Microsyntenic Fasta Sequences with Varying Chromosome Formats 1 I have been working on analyzing microsyntenic regions between different species using the OMA Python API (github.com/DessimozLab/pyomadb). Now I would like to download the fasta sequences of these regions with a script, but it seems that the chromosome formats vary across…

Continue Reading Downloading Microsyntenic Fasta Sequences with Varying Chromosome Formats

search for intron conservancy across species

I’m working with a non-model organism, and I would like to test the conservancy of the new introns I found (or orthologs genes). Do you know any tool and/or database to do that? I’ve tried many databases, such as [OrthoDB][1], [OMA][2], [IAOD][3], and [IntronDB][4] (is not working), but I have…

Continue Reading search for intron conservancy across species

How to input margin to UpsetR figure

How to input margin to UpsetR figure 0 I made upset plot and add a margin with par() , but par() did not work. I used code like below. Could you some give advices? “` p_upset <- upset(fromList(data), order.by = “freq”, keep.order = TRUE, point.size = 5, line.size = 2,…

Continue Reading How to input margin to UpsetR figure

oma orthology part 2 script

oma orthology part 2 script 0 I am running oma to find orthologs between two species of cyanobacteria (Croco and Tricho). I’m using the cheat sheet to run oma-part2.sh on an HPC, but am confused about if/when the job has finished. Only one job array is still running. Some of…

Continue Reading oma orthology part 2 script

Postdoctoral Research position in Bioinformatics and Comparative Genomics

PostDoc position We are looking for a highly motivated individual to join the team of Natasha Glover and Christophe Dessimoz as a Postdoctoral Researcher in Comparative Genomics (lab.dessimoz.org/). This position offers a unique opportunity to contribute to cutting-edge research projects focused in bioinformatics and comparative genomics and to collaborate with…

Continue Reading Postdoctoral Research position in Bioinformatics and Comparative Genomics

Postdoc Position in Comparative Genomics/Bioinformatics; Project about Synteny, Orthology, Evolution, Gene loss and Tomato at UNIL, Switzerland

Postdoctoral Research position in Bioinformatics and Comparative Genomics, Introduction: UNIL is a leading international teaching and research institution, with over 5,000 employees and 17,000 students split between its Dorigny campus, CHUV and Epalinges. As an employer, UNIL encourages excellence, individual recognition and responsibility. Presentation: We are looking for a…

Continue Reading Postdoc Position in Comparative Genomics/Bioinformatics; Project about Synteny, Orthology, Evolution, Gene loss and Tomato at UNIL, Switzerland

How to get the gene ID

There is a brute force method for this. You could upload the fasta sequence in tblastn and keep a filter of 100% sequence cover and blast. Usually the first hit should give you the Genbank/Refsec ID for your protein sequence. The next one will require some scripting, but if you…

Continue Reading How to get the gene ID

Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree

State-of-the-art phylogenomic pipelines require many steps, which can be both time consuming and error prone (Fig. 1a). With Read2Tree, we directly process raw sequencing reads and reconstruct sequence alignments for conventional tree inference methods (Fig. 1b and Supplementary Fig. 1). We start by aligning raw reads to nucleotide sequences derived…

Continue Reading Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree

Structure of anhydrotetracycline-bound Tet(X6) reveals the mechanism for inhibition of type 1 tetracycline destructases

Tet(X6) contains a conserved architecture of type 1 tetracycline destructases We determined the X-ray structure of Tet(X6) at 2.2 Å resolution with Rfree/Rwork of 0.22/0.19 (Table 1). This FAD complexed, anhydrotetracycline-free enzyme structure consists of a conserved architecture for type 1 TDases: a characteristic Rossman fold containing an FAD-binding domain, a…

Continue Reading Structure of anhydrotetracycline-bound Tet(X6) reveals the mechanism for inhibition of type 1 tetracycline destructases

The little skate genome and the evolutionary emergence of wing-like fins

Nakamura, T. et al. Molecular mechanisms underlying the exceptional adaptations of batoid fins. Proc. Natl Acad. Sci. USA 112, 15940–15945 (2015). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Turner, N. et al. The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids. Proc. Biol. Sci….

Continue Reading The little skate genome and the evolutionary emergence of wing-like fins

syntax errors when running part3 all-against-all

Hello, I downloaded a set of precomputed 50 genomes. I successfully completed the oma run and have results. I then added in a new genome and reran. The blasts seem to have run fine. Now when oma is reading the all against all files I am getting syntax errors. Because…

Continue Reading syntax errors when running part3 all-against-all

Probing the Mammalian Mitochondrial Nucleoid

dc.contributor.author Rajala, Nina dc.date.accessioned 2015-04-29T04:47:49Z dc.date.available 2015-04-29T04:47:49Z dc.date.issued 2015 dc.identifier.isbn 978-951-44-9794-0 – dc.identifier.uri trepo.tuni.fi/handle/10024/96996 dc.description.abstract Mitokondrioiden tärkein tehtävä on energian tuottaminen. Mitokondriot ovat solujen hengityskeskuksia, joissa 90 % tarvitsemastamme energiasta tuotetaan oksidatiivisen fosforylaation kautta elektroninsiirtoketjua apuna käyttäen. Kun mitokondriot eivät toimi kunnolla, tuloksena voi olla energiakriisi, erityisesti lihaksissa, aivoissa ja…

Continue Reading Probing the Mammalian Mitochondrial Nucleoid

Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

Continue Reading Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

OMA speed

OMA speed 0 Is there any way to speed up the execution without using parallel processes? The parallel execution does not run well on the system I access. My goal is to compute orthologs between two species, one having 55,725 transcripts, and the other 91.249. It is taking several weeks….

Continue Reading OMA speed

HOG without numbering in the genome of the ancestor reconstructed using the pyHAM

Dear colleagues, Recently I successfully complete OMA standalone run and now I am trying to analyze results using the pyHam python package. The main task for me is to reconstruct the genome of the ancestor of the analyzed species. After executing the following commands, I get information that in the…

Continue Reading HOG without numbering in the genome of the ancestor reconstructed using the pyHAM