Tag: Pfam

KEGG T01003: 286761

Entry 286761            CDS       T01003                                  Symbol Vcpip1 Name (RefSeq) deubiquitinating protein VCPIP1   KO K11861   deubiquitinating protein VCIP135 [EC:3.4.19.12] Organism rno  Rattus norvegicus (rat) Brite KEGG Orthology (KO) [BR:rno00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:rno01002]    286761 (Vcpip1)  09182 Protein families: genetic information processing   04121 Ubiquitin system [BR:rno04121]    286761 (Vcpip1)Enzymes [BR:rno01000] 3. Hydrolases  3.4  Acting on peptide bonds (peptidases)   3.4.19  Omega peptidases    3.4.19.12  ubiquitinyl…

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MAFFT benchmark

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…

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Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species

Tan, M. H. et al. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci. Rep. 9, 1–16 (2019). ADS  Google Scholar  Zhang, Y. et al. Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida). Mol. Phylogenet. Evol. 125, 220–231 (2018). CAS  PubMed  Google…

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Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

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Google Researchers Use Machine Learning Approach To Annotate Protein Domains

Source: www.nature.com/articles/s41587-021-01179-w.epdf Proteins play an important part in the construction and function of all living organisms. Each protein is made up of a chain of amino acid building blocks. Much like an image might have numerous things, a protein can have multiple components, known as protein domains. Researchers have been…

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The long non-coding RNA LNC_000397 negatively regulates PRRSV replication through induction of interferon-stimulated genes | Virology Journal

Badaoui B, Rutigliano T, Anselmo A, Vanhee M, Nauwynck H, Giuffra E, Botti S. RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence. PLOS ONE. 2014;9:91918. Article  Google Scholar  Bateman A, Birney E, Cerruti L, Durbin R, Etwiller…

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KEGG T01001: 5105

Entry 5106              CDS       T01001                                  Symbol PCK2, PEPCK, PEPCK-M, PEPCK2 Name (RefSeq) phosphoenolpyruvate carboxykinase 2, mitochondrial   KO K01596   phosphoenolpyruvate carboxykinase (GTP) [EC:4.1.1.32] Organism hsa  Homo sapiens (human) Pathway hsa00010   Glycolysis / Gluconeogenesis hsa00020   Citrate cycle (TCA cycle) hsa00620   Pyruvate metabolism hsa01100   Metabolic pathways hsa03320   PPAR signaling pathway hsa04068   FoxO signaling pathway hsa04151   PI3K-Akt signaling…

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KEGG T03334: R50912_07385

Entry R50912_23945      CDS       T03334                                  Name (GenBank) alpha-galactosidase   KO K07407   alpha-galactosidase [EC:3.2.1.22] Organism paeq  Paenibacillus sp. FSL R5-0912 Pathway paeq00052   Galactose metabolism paeq00561   Glycerolipid metabolism paeq00600   Sphingolipid metabolism paeq01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:paeq00001] 09100 Metabolism  09101 Carbohydrate metabolism   00052 Galactose metabolism    R50912_23945  09103 Lipid metabolism   00561 Glycerolipid metabolism    R50912_23945   00600 Sphingolipid metabolism    R50912_23945Enzymes [BR:paeq01000] 3. Hydrolases  3.2  Glycosylases   3.2.1  Glycosidases, i.e. enzymes that hydrolyse O-…

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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;…

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KEGG T00007: b1542

Entry b4323             CDS       T00007                                  Symbol uxuB Name (RefSeq) D-mannonate oxidoreductase   KO K00040   fructuronate reductase [EC:1.1.1.57] Organism eco  Escherichia coli K-12 MG1655 Pathway eco00040   Pentose and glucuronate interconversions eco01100   Metabolic pathways Module eco_M00061   D-Glucuronate degradation, D-glucuronate => pyruvate + D-glyceraldehyde 3P Brite KEGG Orthology (KO) [BR:eco00001] 09100 Metabolism  09101 Carbohydrate metabolism   00040 Pentose and glucuronate interconversions    b4323 (uxuB)Enzymes…

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KEGG T01005: 453503

Entry 453503            CDS       T01005                                  Symbol SNX1 Name (RefSeq) sorting nexin-1 isoform X3   KO K17917   sorting nexin-1/2 Organism ptr  Pan troglodytes (chimpanzee) Pathway ptr04144   Endocytosis Brite KEGG Orthology (KO) [BR:ptr00001] 09140 Cellular Processes  09141 Transport and catabolism   04144 Endocytosis    453503 (SNX1) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:ptr04131]    453503 (SNX1)  09183 Protein families: signaling and cellular processes   04990…

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Senior Bioinformatics Scientist II/ Staff Bioinformatics Scientist

Inscripta was founded in 2015 and recently launched the world’s first benchtop Digital Genome Engineering platform. The company is growing aggressively, investing in its leadership, team, and technology with a recent $150mm financing round led by Fidelity and TRowe price. The company’s advanced CRISPR-based platform, consisting of an instrument, reagents,…

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pfam_scan.pl can’t find the pfamdb

pfam_scan.pl can’t find the pfamdb 1 I am trying to run pfam_scan.pl script which keep generating this error below though both Pfam-A.hmm and Pfam-A.hmm.dat files are in /pfamdb. Can someone please help me identify the errors and resolve this? perl /media/owner/b45f8e7a-003c-4573-8841-bcb5f76f281f/sn/rgaugury/PfamScan/pfam_scan.pl -fasta Hannuus_494_r1.2.protein.fa -dir /media/owner/b45f8e7a-003c-4573-8841-bcb5f76f281f/sn/rgaugury/database/pfamdb FATAL: can’t find “Pfam-A.hmm” and/or…

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Probe annotation file for microarray platform MoGene-1_0-st-v1

Hi, I would use the pre-built Bioconductor annotation databases / packages for this array (I have used this array a few times over the years): mogene10sttranscriptcluster.db mogene10stprobeset.db Most likely mogene10sttranscriptcluster.db is what you want: require(mogene10sttranscriptcluster.db) columns(mogene10sttranscriptcluster.db) [6] “ENTREZID” “ENZYME” “EVIDENCE” “EVIDENCEALL” “GENENAME” [11] “GO” “GOALL” “IPI” “MGI” “ONTOLOGY” [16] “ONTOLOGYALL”…

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A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest

1. Edmonds, R. L. & Eglitis, A. The role of the Douglas-fir beetle and wood borers in the decomposition of and nutrient release from Douglas-fir logs. Can. J. Res. 19, 853–859 (1989). Article  Google Scholar  2. Hlásny, T. et al. Living with bark beetles: impacts, outlook and management options. In:…

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Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

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…

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get only one representative fasta sequence per family

Pfam – get only one representative fasta sequence per family 2 Hey can u help me with getting only one representative fasta sequence per family? Is there way to simply do that? cheers X pfam fasta protein • 186 views It’s not trivial. You could use the sequences from the…

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Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance

1. Lee, M.-R. et al. Mycobacterium abscessus complex infections in humans. Emerg. Infect. Dis. 21, 1638–1646 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Prince, D. S. et al. Infection with Mycobacterium avium complex in patients without predisposing conditions. N. Engl. J. Med. 321, 863–868 (1989). CAS  PubMed  Article  Google…

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Answer: alphafold online availability and use case

1. There is no need for heavy-duty methods such as AlphaFold2 (AF2) in all cases. It is very unlikely that you have 1500 sequences that only have domains of unknown function, and even if you do, there were successful structure prediction servers in existence before AF2. So even though what…

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Pooling annotations from different databases in InterProScan

Pooling annotations from different databases in InterProScan 0 Is it acceptable to pool the annotations from the various sources InterProScan offers, and annotate a sequence with a subset of these? For example, if I have something like so: id annot src start stop seq1 dom1 Pfam 100 120 seq1 dom1a…

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