Categories
Tag: InterPro
Curated model organism gene functional annotations
Curated model organism gene functional annotations 0 Hi, I’m working with a model organism for the first time – C. elegans nematodes – and have created a list of differential expressed genes from some RNAseq data the lab had. One of the things I like to do is look for…
Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses
Honegger, R. The lichen symbiosis: What is so spectacular about it?. Lichenologist 30, 193–212 (1998). Article Google Scholar Grube, M. & Berg, G. Microbial consortia of bacteria and fungi with focus on the lichen symbiosis. Fung. Biol. Rev. 23, 72–85 (2009). Article Google Scholar Spribille, T. et al. Basidiomycete yeasts…
How to get multiple protein domain database domain name from id’s
How to get multiple protein domain database domain name from id’s 0 Hello i got a blast2go output with a column with id’s from multiple databases suported by interpro but i need the domain names so i can filter the data someone know how can i do it? My data…
Computational and bioinformatics tools for life sciences
In recent decades, the development of computational and bioinformatics tools and websites for life sciences has increased exponentially. This great development has gone hand in hand with the availability of genome, proteome and macromolecule structure databases, and also of functional experiments, including microarray and RNAseq expression data, RNA-protein interactions, ChIP-seq,…
Chromosome-scale genome of the human blood fluke Schistosoma mekongi and its implications for public health | Infectious Diseases of Poverty
Barnett R. Schistosomiasis. (1474–547X (Electronic)). Steinmann P, Keiser J, Bos R, Tanner M, Utzinger J. Schistosomiasis and water resources development: systematic review, meta-analysis, and estimates of people at risk. Lancet Infect Dis. 2006;6(7):411–25. Article PubMed Google Scholar Uthailak N, Adisakwattana P, Thiangtrongjit T, Limpanont Y, Chusongsang P, Chusongsang Y, et…
Estimating the proportion of nonsense variants undergoing the newly described phenomenon of manufactured splice rescue
Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405–24. Article PubMed Google Scholar Abou…
EMDB < EMD-14025
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
EMDB < EMD-16930
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Prediction of alternative pre-mRNA splicing outcomes
RiboSplitter pipeline Figure 1 shows a flowchart of the pipeline (see “Methods” for details). The key insight in RiboSplitter is to initially go small and predict the reading frame of the first 5´ exon of the splicing event, instead of trying to translate the full isoform. This is because the full…
EMDB < Search results
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
UniProt: A0A8U0V2F9_MUSPF
ID A0A8U0V2F9_MUSPF Unreviewed; 413 AA. AC A0A8U0V2F9; DT 12-OCT-2022, integrated into UniProtKB/TrEMBL. DT 12-OCT-2022, sequence version 1. DT 03-MAY-2023, entry version 4. DE SubName: Full=Protein C-ets-1 isoform X5 {ECO:0000313|RefSeq:XP_044936298.1}; GN Name=ETS1 {ECO:0000313|RefSeq:XP_044936298.1}; OS Mustela putorius furo (European domestic ferret) (Mustela furo). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC…
Chromosome-level genomes of three key Allium crops and their trait evolution
Chase, M. W. et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20 (2016). Article Google Scholar Jones, M. G. et al. Biosynthesis of the flavour precursors of onion and garlic. J. Exp. Bot….
Mapping Mutations, Protein Domains, Exon structure on a Protein Figure/Visualization with annoations
Mapping Mutations, Protein Domains, Exon structure on a Protein Figure/Visualization with annoations 2 I want to make a figure of a protein with annotated mutations, exon number, and protein domains. MutationMapper on cbioportal is god but it lacks protein annotations that I find in InterPro. I know this was asked…
ftsj3 Summary
Gene Symbol: ftsj3 Gene Name: FtsJ RNA methyltransferase homolog 3 Synonyms: ( Nomenclature history ) Gene Function: Putative SAM-dependent rRNmethyltransferase SPB1 Protein Function : Probable…
EMDB < EMD-40454
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Bioinformatics analysis of Uncyclotides: a potential antimicrobial peptide to protect against heart failure diseases
Abstract Heart failure (also known as HF) is a clinical disorder triggered by functional and structural defects in cardiac muscles causing blood ejection or damage of ventricular filling. Even though the progression in the field of medicine, HF control, which generally presents as a syndrome, has been a task to…
EMDB < EMD-25228
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Distantly related Alteromonas bacteriophages share tail fibers exhibiting properties of transient chaperone caps
de Jonge, P. A., Nobrega, F. L., Brouns, S. J. J. & Dutilh, B. E. Molecular and evolutionary determinants of bacteriophage host range. Trends Microbiol. 27, 51–63 (2019). Article PubMed Google Scholar Cambillau, C. Bacteriophage module reshuffling results in adaptive host range as exemplified by the baseplate model of listerial…
EMBL-EBI Training course | Metagenomics bioinformatics at MGnify
Learn about the tools, processes, and analysis approaches used by MGnify in the field of genome-resolved metagenomics. This course will cover the use of publicly available resources to manage, share, analyse, and interpret metagenomics data, focussing primarily on the assembly-based approaches used in MGnify analysis. The delivered content will involve…
Genome sequence and annotation of Periconia digitata a hopeful biocontrol agent of phytopathogenic oomycetes
Strain identification The strain Phoma sp. CNCM I-4278 was previously isolated from the rhizosphere of Nicotiana tabacum (cv Xanthi, Solanaceae) grown under controlled conditions17. The fungus was identified according to the closest similarity of its 18 S rRNA sequence (HM16174323) with those present in GenBank by that time and it was…
UniProt: A0A7F8Q8W3_LEPWE
ID A0A7F8Q8W3_LEPWE Unreviewed; 479 AA. AC A0A7F8Q8W3; DT 10-FEB-2021, integrated into UniProtKB/TrEMBL. DT 10-FEB-2021, sequence version 1. DT 03-MAY-2023, entry version 8. DE SubName: Full=Protein FAM118A isoform X2 {ECO:0000313|RefSeq:XP_030877677.1}; GN Name=FAM118A {ECO:0000313|RefSeq:XP_030877677.1}; OS Leptonychotes weddellii (Weddell seal) (Otaria weddellii). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Laurasiatheria;…
UniProt: A0A6J2VJ84_CHACN
ID A0A6J2VJ84_CHACN Unreviewed; 220 AA. AC A0A6J2VJ84; DT 07-OCT-2020, integrated into UniProtKB/TrEMBL. DT 07-OCT-2020, sequence version 1. DT 28-JUN-2023, entry version 11. DE SubName: Full=Claudin-4-like {ECO:0000313|RefSeq:XP_030632049.1}; GN Name=LOC115813661 {ECO:0000313|RefSeq:XP_030632049.1}; OS Chanos chanos (Milkfish) (Mugil chanos). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Gonorynchiformes; OC Chanidae;…
EMDB < EMD-40539
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Bioinformatics Developer – Hinxton, United Kingdom – European Molecular Biology Laboratory (EMBL)
Description About the team/job We are seeking a highly motivated and skilled Bioinformatics Developer to join the InterPro team, which is part of the Sequence Family Resources led by Alex Bateman. InterPro is a core protein data resource that plays a vital role in the classification of protein domains and…
Exploring protein families and domains using InterPro
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites using predictive models provided by 13 different databases. This webinar will take you through the different ways to search the InterPro website and its API to identify protein families and domains….
EMDB < EMD-12919
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Multi-omic analyses reveal the unique properties of chia (Salvia hispanica) seed metabolism
Harley, R. M. et al. Labiatae. in Flowering Plants · Dicotyledons. The Families and Genera of Vascular Plants (ed. Kadereit, J. W.) vol. 7 167–275 (2004). Kokkini, S., Karousou, R. & Hanlidou, E. HERBS | Herbs of the Labiatae. Encyclopedia of Food Sciences and Nutrition 3082–3090 (2003) doi.org/10.1016/B0-12-227055-X/00593-9. Hao, D….
Pan-cancer structurome reveals overrepresentation of beta sandwiches and underrepresentation of alpha helical domains
AlphaFold models significantly expanded structural space of over and underexpressed protein-coding genes in 21 cancer types Our non-redundant sets of over and underexpressed protein-coding genes for all cancer types include 5341 and 7320 genes, respectively. Figure 1A, B illustrates the availability of known 3D structures (PDB) and AlphaFold models (AF). For…
Interpro Enrichment – Any Organism
Interpro Enrichment – Any Organism 3 Among many tools for over-/under-representation analysis there are few which are not constrained to fixed list of species. For my knowledge it is Ontologizer and ASCA-Functional from SEA suite. There one have to just provide already available association of genes with functional categories. I…
EMDB < EMD-33674
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Glutamine synthetase (GS) knockout (KO) using CRISPR/Cpf1 diversely enhances selection efficiency of CHO cells expressing therapeutic antibodies
Identification and expression of GS genes in CHO cells Database analysis (see Supplementary information 1 indicated that the endogenous GS genes in CHO-K1 include two genes on chromosome 5 (GS5) and chromosome 1 (GS1), for which in-house RNAseq data and previous publication, listed in Supplementary Table S1, showed high and low…
The genome of Acorus deciphers insights into early monocot evolution
Lughadha, E. N. et al. Counting counts: revised estimates of numbers of accepted species of flowering plants, seed plants, vascular plants and land plants with a review of other recent estimates. Phytotaxa 272, 82–88 (2016). Article Google Scholar Group, A. P. An update of the Angiosperm Phylogeny Group classification for…
Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants
Awasthi MK, Singh E, Binod P, Sindhu R, Sarsaiya S, Kumar A, et al. Biotechnological strategies for bio-transforming biosolid into resources toward circular bio-economy: a review. Renew Sustain Energy Rev. 2022;156:111987. Article CAS Google Scholar Diamantis V, Eftaxias A, Stamatelatou K, Noutsopoulos C, Vlachokostas C, Aivasidis A. Bioenergy in the…
Gap-free genome assembly of anadromous Coilia nasus
Yang, Q. L., Gao, T. X. & Miao, Z. Q. Differentiation between populations of Japanese grenadier anchovy (Coilia nasus) in Northwestern Pacific based on ISSR markers: Implications for biogeography. Biochem Syst and Ecol 39, 286–296 (2011). CAS Google Scholar Shen, H. S. et al. In-depth transcriptome analysis of Coilia ectenes,…
File:LINE-1 Retrotransposon ORF2p.png – Wikipedia
From Wikipedia, the free encyclopedia Summary DescriptionLINE-1 Retrotransposon ORF2p.png English: www.ebi.ac.uk/interpro/protein/reviewed/O00370/ Has reverse transcriptase activity required for target-primed reverse transcription of the LINE-1 element mRNA, a crucial step in LINE-1 retrotransposition. Date 24 May 2023 Source alphafold.ebi.ac.uk/entry/O00370 Author Jumper, J et al. Highly accurate protein structure prediction with AlphaFold. Nature…
EMDB < EMD-17118
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation
Hunt, T. et al. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318, 1913–1916 (2007). Article ADS CAS PubMed Google Scholar Crowson, R. A. The phylogeny of coleoptera. Annu. Rev. Entomol. 5, 111–134 (1960). Article Google Scholar Darwin, C. The Descent of Man, and Selection…
EMDB < EMD-10691
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase
Mutant collection development We mutagenized 2,700 seeds of the wheat–Th. elongatum introgression line RWG34 containing Sr43 (ref. 29). Dry seeds were incubated for 16 h with 200 ml of a 0.8% (w/v) EMS solution with constant shaking on a Roller Mixer (Model SRT1, Stuart Scientific) to ensure maximum homogenous exposure of the…
Get protein information from ensemblbacteria using interpro
Get protein information from ensemblbacteria using interpro 1 So I am trying to access protein information using interpro ids on ensemblbacteria. I have written a MySQL code in R however, I can’t quite figure out how to get protein information using the ids using programming language. I have put in…
Apoptotic gene loss in Cnidaria is associated with transition to parasitism
Elmore, S. Apoptosis: A review of programmed cell death. Toxicol. Pathol. 35, 495–516 (2007). Article CAS PubMed PubMed Central Google Scholar Shi, Y. Caspase activation, inhibition, and reactivation: A mechanistic view. Protein Sci. 13, 1979–1987 (2004). Article CAS PubMed PubMed Central Google Scholar Alberts, B., Johnson, A. & Lewis, J….
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…
UniProt: A0A2Y9QLR8_TRIMA
ID A0A2Y9QLR8_TRIMA Unreviewed; 522 AA. AC A0A2Y9QLR8; DT 12-SEP-2018, integrated into UniProtKB/TrEMBL. DT 12-SEP-2018, sequence version 1. DT 22-FEB-2023, entry version 12. DE SubName: Full=actin-binding protein IPP isoform X2 {ECO:0000313|RefSeq:XP_023582882.1}; GN Name=LOC101351470 {ECO:0000313|RefSeq:XP_023582882.1}; OS Trichechus manatus latirostris (Florida manatee). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Afrotheria;…
A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila)
Ethics statement All animal experimental procedures were approved by the Biomedical Ethics Committee of Qufu Normal University (approval number: 2022001). Sampling and sequening The experimental sample is a wounded male duck found during the wild bird survey in Jiangsu, China, which died unexpectedly during rescue. We dissected the sample and…
EMDB < EMD-16884
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
EMDB < EMD-29544
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
UniProt: A0A6P7ILG0_9TELE
ID A0A6P7ILG0_9TELE Unreviewed; 421 AA. AC A0A6P7ILG0; DT 02-DEC-2020, integrated into UniProtKB/TrEMBL. DT 02-DEC-2020, sequence version 1. DT 22-FEB-2023, entry version 9. DE SubName: Full=transcriptional enhancer factor TEF-5 isoform X8 {ECO:0000313|RefSeq:XP_028261144.1}; GN Name=tead3 {ECO:0000313|RefSeq:XP_028261144.1}; OS Parambassis ranga (Indian glassy fish). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Actinopterygii; Neopterygii;…
UniProt: A0A6P8XQ90_DROAB
ID A0A6P8XQ90_DROAB Unreviewed; 717 AA. AC A0A6P8XQ90; DT 02-DEC-2020, integrated into UniProtKB/TrEMBL. DT 02-DEC-2020, sequence version 1. DT 22-FEB-2023, entry version 9. DE SubName: Full=RUN and FYVE domain-containing protein 2 isoform X5 {ECO:0000313|RefSeq:XP_034113470.1}; GN Name=LOC117574004 {ECO:0000313|RefSeq:XP_034113470.1}; OS Drosophila albomicans (Fruit fly). OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; OC…
EMDB < EMD-14480
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
EMDB < EMD-15267
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding
FAO. Faostat: FAO Statistical Databases. (Food & Agriculture Organization of the United Nations (FAO), 2000). The war in Ukraine is exposing gaps in the world’s food-systems research. Nature 604, 217–218 (2022). Chapman, M. A., He, Y. & Zhou, M. Beyond a reference genome: pangenomes and population genomics of underutilized and…
Problem running interproscan-5.15-54.0 for protein sequences
Hello, I am using the standalone interproscan-5.15-54.0. I could run the given test_proteins file sucessfully however, when I am trying to run my protein sequences, it gives same errors. This is the sam question in biostar (Problem running interproscan-5.14-53.0 for protein sequences), but I can’t find any useful information. Please…
how to get pfam id of proteins belonging to a particular family along with sequences in that family?
how to get pfam id of proteins belonging to a particular family along with sequences in that family? 1 Hello, i am a newbie in bioinformatics I am trying to get protein sequences of a particular species e.g homo sapiens along with the pfam id of the family to which…
Solved Can you explain to me important aspects of this
Can you explain to me important aspects of this genbank Bos taurus partial gdf-8 for myostatin and promoter region GenBank: AJ438578.1 FASTA Graphics Go to: LOCUS AJ438578 1269 bp DNA linear MAM 26-JUL-2016 DEFINITION Bos taurus partial gdf-8 for myostatin and promoter region. ACCESSION AJ438578 VERSION AJ438578.1 KEYWORDS gdf-8; myostatin….
EMDB < EMD-20232
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
EMDB < EMD-28585
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Maternal diet induces persistent DNA methylation changes in the muscle of beef calves
Gicquel, C., El-Osta, A. & Le Bouc, Y. Epigenetic regulation and fetal programming. Best Pract. Res. Clin. Endocrinol. Metab. 22, 1–16 (2008). CAS Google Scholar Godfrey, K. M. & Barker, D. J. Fetal programming and adult health. Public Health Nutr. 4, 611–624 (2001). CAS Google Scholar Encinias, H. B., Lardy,…
EMDB < EMD-13594
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis
Data collection Metagenomic project information was collected from the MGnify metagenomic database31. Currently (September 2021), microbiome data (sequence, taxonomic, and functional information, etc.) of 325,323 environmental samples can be found in this database. Often, microbes from similar ecological communities have been studied by different groups at different times and locations….
EMDB < EMD-20433
Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…
Empathy List Archives
Dear colleagues, Data on sequence level mapping through the SIFTS process www.ebi.ac.uk/pdbe/docs/sifts/ can now be retrieved directly from updated mmCIF files, available on PDBe entry pages. These files now contain residue-level mapping between UniProt and PDB entries, including coordinate numbering for UniProt accessions and mapping to a host of other…
UniProt: A0A6I9ZUN5_ACIJB
ID A0A6I9ZUN5_ACIJB Unreviewed; 234 AA. AC A0A6I9ZUN5; DT 07-OCT-2020, integrated into UniProtKB/TrEMBL. DT 07-OCT-2020, sequence version 1. DT 25-MAY-2022, entry version 6. DE SubName: Full=tumor necrosis factor ligand superfamily member 8 {ECO:0000313|RefSeq:XP_014931799.1}; GN Name=TNFSF8 {ECO:0000313|RefSeq:XP_014931799.1}; OS Acinonyx jubatus (Cheetah). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Laurasiatheria;…
Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis
Hallam, S. J., Goncharov, A., McEwen, J., Baran, R. & Jin, Y. Syd-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains specifies axon identity in C. elegans. Nat. Neurosci. 5, 1137–1146 (2002). CAS PubMed Google Scholar Xu, Y. & Quinn, C. C. SYD-1 promotes multiple developmental steps leading to…
Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis
INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…
UniProt: A0A1S3QEZ7_SALSA
ID A0A1S3QEZ7_SALSA Unreviewed; 104 AA. AC A0A1S3QEZ7; DT 12-APR-2017, integrated into UniProtKB/TrEMBL. DT 12-APR-2017, sequence version 1. DT 02-JUN-2021, entry version 11. DE SubName: Full=lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog isoform X2 {ECO:0000313|RefSeq:XP_014038412.1}; GN Name=LOC106591717 {ECO:0000313|RefSeq:XP_014038412.1}; OS Salmo salar (Atlantic salmon). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Actinopterygii;…
dCas9-VPR-mediated transcriptional activation of functionally equivalent genes for gene therapy
1. Dunbar, C. E. et al. Gene therapy comes of age. Science 359, eaan4672 (2018). PubMed Google Scholar 2. Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019). CAS PubMed PubMed Central Google Scholar 3. Eid, A.,…
Batch conversion of InterPro IDs to GO IDS for TopGO analysis
Batch conversion of InterPro IDs to GO IDS for TopGO analysis 0 Hi all, I have a list of about two thousand InterPro IDs that I would like to convert to their corresponding GO IDs for subsequent enrichment analyses in TopGO. I initially used the Interpro2go batch text file to…
Using protein domains for annotation validation
Using protein domains for annotation validation 0 I am trying to develop a procedure for assessing the reliability of proteins derived from a genome annotation analysis. One thing I’d like to do is search the annotated protein for protein domains, with the idea being that proteins containing known domains are…
Converting an S4 object into a dataframe in R
I have an S4 object named ‘res’ which I got while using an R package called RDAVIDWebService. I can’t seem to find a way to convert this object into a dataframe in R. I tried using the function ‘as.data.frame(res)’ but it throws this error: > as.data.frame(res) Error in as.data.frame.default(res) :…