Tag: InterProScan
amrfinder not working on loop?
amrfinder not working on loop? 0 Hi, i am trying to run amrfinder on multiple genome as in loop, and it gives following error, and whatever input file I am using in this program are also not shown after it run. #!/bin/bash **for k in /home/bvs/neelam/AMRFINDER_hypo/hyocool/*.fasta;do NAME=$(basename $k .fasta) echo…
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,…
Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales
Genome sequencing and assembly We sequenced and assembled genomes for the sandalwood species S. album and S. yasi (Fig. 1). In total, ~23 Gb and ~25 Gb of clean short reads of S. album and S. yasi were obtained for the genomic survey, respectively (Supplementary Tables 1 and 2). According to k-mer analysis, the…
I don’t want to believe the Interproscan DB estimated download time.
I don’t want to believe the Interproscan DB estimated download time. 0 Interproscan in Blast2go is too slow, so I am trying to I am trying to download the Interproscan DB at the same time as scanning against the CDD and HMMPfam DB only. here: interproscan-docs.readthedocs.io/en/latest/LocalLookupService.html Two hours after starting…
The first high-quality chromosome-level genome of the Sipuncula Sipunculus nudus using HiFi and Hi-C data
Cutler, E. B. The Sipuncula: Their Systematics, Biology, And Evolution (New York: Cornell University Press, doi.org/10.7591/9781501723643, 1994) Nielsen, C. Some aspects of spiralian development. Acta Zool. 91, 20–28, doi.org/10.1111/j.1463-6395.2009.00421.x (2010). Article Google Scholar Huang, D. Y., Chen, J. Y., Vannier, J. & Saiz Salinas, J. I. Early Cambrian sipunculan worms…
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….
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…
An ancient metalloenzyme evolves through metal preference modulation
Jayaraman, V., Toledo-Patino, S., Noda-Garcia, L. & Laurino, P. Mechanisms of protein evolution. Protein Sci. 31, e4362 (2022). Article CAS PubMed Google Scholar Huang, R. et al. Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates. Proc. Natl Acad. Sci. USA 109, 2966–2971 (2012). Article CAS PubMed PubMed Central …
GO enrichment analysis
GO enrichment analysis 1 Hello, I would like to perform GO enrichment analysis. My data format after deseq analysis as following image which contains deseq-related factors and functional annotation (accession id based on nrdatabase as well as arabidopsis) also with GO id generated from interproscan. with this information, which tools…
Salamandra salamandra homology annotation blastp-swissprot
Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Mounting evidence is showing that attitude to disperse is unevenly distributed among individuals within animal populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here,…
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…
Functional metagenomics uncovers nitrile-hydrolysing enzymes in a coal metagenome
Introduction Cyanide-containing compounds are known as nitriles and are widely distributed in the natural environment. They are generated by different plants in various forms, such as ricinine, phenyl acetonitrile, cyanogenic glycosides, and β -cyanoalanine (Sewell et al., 2003). Anthropogenic activities have substantially influenced the production of vast quantities of nitrile…
Filter InterProScan output for a specific function
Filter InterProScan output for a specific function 0 I am working with metagenomic data. After running InterProScan (IPS), I want to get only the genes related to a function (for example lipid-active enzymes). I know that there are some databases that only focus on a group of genes (like CAZy,…
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….
Characterization, genome analysis and genetic tractability studies of a new nanocellulose producing Komagataeibacter intermedius isolate
Isolation, characterization and classification of BC-producing strain Isolation of single clones from CaCO3 halo zones in Glucose-Yeast Extract-Calcium carbonate agar and iterated subculturing in HS-Glu agar resulted in enrichment of an isolate with beige-coloured, smooth-edged and umbonate shaped colonies characteristics (Fig. S1A). The isolate is hereafter called ‘ENS15’. Under 100X magnification,…
The evolutionary origin of host association in the Rickettsiales
Salje, J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat. Rev. Microbiol. 19, 375–390 (2021). CAS PubMed Article Google Scholar Wang, S. & Luo, H. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nat. Commun. 12, 3324 (2021). CAS PubMed PubMed Central Article Google Scholar Strassert, J. F. H.,…
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses
Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017). CAS PubMed Article Google Scholar Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J. & Embley, T. M. Phylogenomics provides robust support for a two-domains tree of life. Nat. Ecol….
Ubuntu Manpage: Bio::Tools::Seg – parse “seg” output
Provided by: libbio-perl-perl_1.7.2-2_all NAME Bio::Tools::Seg – parse “seg” output SYNOPSIS use Bio::Tools::Seg; my $parser = Bio::Tools::Seg->(-file => ‘seg.fasta’); while ( my $f = $parser->next_result ) { if ($f->score < 1.5) { print $f->location->to_FTstring, ” is low complexity\n”; } } DESCRIPTION “seg” identifies low-complexity regions on a protein sequence. It is…
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…
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…
