Tag: hmmer

How to Create an HMMER Profile with VFDB Files?

How to Create an HMMER Profile with VFDB Files? 1 How do I create an HMM profile using the files from www.mgc.ac.cn/VFs/ to run HMMER? I have the file.faa after running Prodigal and I need to generate a profile with hmmbuild called profile.hmm. This is my first time creating a…

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How to filter hmmer output and get needed enzymes

How to filter hmmer output and get needed enzymes 0 This is a part of my file. You can see the output for KI0314_NODE_20043_length_7522_cov_1.691954_4. Glyco_hydro_43 PF04616.18 KI0314_NODE_20043_length_7522_cov_1.691954_4 – 2.3e-43 148.8 4.0 3.5e-43 148.2 4.0 1.3 1 0 0 1 1 1 1 Glycosyl hydrolases family 43 GH43_C2 PF17851.5 KI0314_NODE_20043_length_7522_cov_1.691954_4 –…

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Comparative genomics and proteomics analysis of phages infecting multi-drug resistant Escherichia coli O177 isolated from cattle faeces

Batinovic, S. et al. Bacteriophages in natural and artificial environments. Pathogens 8, 100. doi.org/10.3390/pathogens8030100 (2019). Article  PubMed  PubMed Central  Google Scholar  Mushegian, A. R. Are there 10^31 virus particles on earth, or more, or fewer?. J. Bacteriol. 202(9), 2020. doi.org/10.1128/JB.00052-20 (2020). Article  Google Scholar  Kutter, E. & Sulakvelidze, A. Bacteriophages:…

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Page not found at /GeneAnnotation/?id=Pzi006309&type=Pzijinensis

Page not found at /GeneAnnotation/?id=Pzi006309&type=Pzijinensis Using the URLconf defined in orchidbase5.urls, Django tried these URL patterns, in this order: ^admin/ ^rec_histone/$ [name=”main_algorithm”] Info_download/$ [name=”Info_download”] Sum_download/$ [name=”Sum_download”] example_download/$ [name=”example_download”] ^ ^$ [name=”home2020″] ^ ^geneinfo2022/ [name=”geneinfo2020″] ^ ^releaseSummary2022/ [name=”releaseSummary2020″] ^ ^orchidSpecies/ [name=”orchidSpecies”] ^ ^Contacts/ [name=”Contacts”] ^ ^Orchidbase4.0_user_guide/ [name=”Orchidbase4_user_guide”] ^ ^Orchidbase5.0_user_guide/ [name=”Orchidbase5_user_guide”] ^…

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A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera

Jiao, Y. N. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100 (2011). Article  PubMed  Google Scholar  Levin, D. A. Polyploidy and novelty in flowering plants. Am. Nat. 122, 1–25 (1983). Article  Google Scholar  Soltis, P. S. & Soltis, D. E. Ancient WGD events as drivers of…

Continue Reading A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera

Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article  ADS  CAS  PubMed  Google Scholar  Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….

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picrust2 installation error on mac m2

I am trying to install Picrust2 on a mac m2 and am getting installation errors regarding incompatible packages (perhaps a type or missing channel).  Looking for: [‘picrust2=2.5.2’] bioconda/osx-arm64                                 124.0 B @ 154.0 B/s  0.8s…

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Building customized database using HHblits

Building customized database using HHblits 1 Hi, Sorry for asking this naive question I have 7000 FASTA sequences (not MSA) and I want to build a customized database of these and search against themselves using HHblits. I am following HH-suite tutorial (github.com/soedinglab/hh-suite/wiki#building-customized-databases) but I am getting an error every time…

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Antiviral type III CRISPR signalling via conjugation of ATP and SAM

Cloning Supplementary Table 1 shows the synthetic gene, DNA and RNA oligonucleotide sequences used in this study. The synthetic genes encoding B.fragilis Cas6, CorA, NrN and C. botulinum SAM lyase purchased as g-blocks (IDT) were codon-optimized for expression in E. coli C43 (DE3) via the vector pEhisV5TEV, which encodes eight…

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How to properly run prokka on Ubuntu 22?

How to properly run prokka on Ubuntu 22? 0 Hello I have installed prokka on Ubuntu 22 with the command sudo apt -y install prokka. The installation seems complete but when I try to set the database I get the error: $ prokka –setupdb [19:13:28] Appending to PATH: /usr/bin [19:13:28]…

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How to properly run prokka on Unbuntu 22?

How to properly run prokka on Unbuntu 22? 0 Hello I have installe prokka on Ubuntu 22 with the command sudo apt -y install prokka. The installation seems complete but when I try to set the database I get the error: $ prokka –setupdb [19:13:28] Appending to PATH: /usr/bin [19:13:28]…

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EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets | BMC Bioinformatics

EasyCGTree was implemented in Perl programming languages (www.perl.org/) and was built using a collection of published reputable tools, including Clustal Omega version 1.2.4 [12]; consense from PHYLIP version 3.698 [13]; FastTree version 2.1 [14]; hmmbuild and hmmsearch from HMMER version 3.0 (hmmer.org/); IQ-TREE version 2.1.1 [15]; trimAl version 1.2 [16];…

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Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples

Tuganbaev, T. et al. Diet diurnally regulates small intestinal microbiome-epithelial-immune homeostasis and enteritis. Cell 182, 1441–1459 (2020). Article  CAS  PubMed  Google Scholar  Dejea, C. M. et al. Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science 359, 592–597 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Bullman,…

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Finding the Homologous sequences

Finding the Homologous sequences 1 Hi, I want to identify the homologs of my seed sequences in large number of proteomes. I know that I can use Blastp, HMMER and some deep learning homology detection tools. Also I could also try to find the domains and GO for filtering the…

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MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data

Real metaHi-C datasets In this study, we leveraged several publicly available metagenomic Hi-C datasets, consisting of two short-read metaHi-C datasets and two long-read metaHi-C datasets. The specific sizes of raw datasets were shown in Supplementary Table 6. Two short-read metaHi-C datasets were generated from different microbial ecosystems, including human gut (BioProject:…

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Page not found at /GeneAnnotation/?id=Peq006601&type=Phalaenopsis

Page not found at /GeneAnnotation/?id=Peq006601&type=Phalaenopsis Using the URLconf defined in orchidbase5.urls, Django tried these URL patterns, in this order: ^admin/ ^rec_histone/$ [name=”main_algorithm”] Info_download/$ [name=”Info_download”] Sum_download/$ [name=”Sum_download”] example_download/$ [name=”example_download”] ^ ^$ [name=”home2020″] ^ ^geneinfo2022/ [name=”geneinfo2020″] ^ ^releaseSummary2022/ [name=”releaseSummary2020″] ^ ^orchidSpecies/ [name=”orchidSpecies”] ^ ^Contacts/ [name=”Contacts”] ^ ^Orchidbase4.0_user_guide/ [name=”Orchidbase4_user_guide”] ^ ^Orchidbase5.0_user_guide/ [name=”Orchidbase5_user_guide”] ^…

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A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil

Field sample collection Topsoil samples (0–15 cm, roughly 0.5 m3) from replicate field plots were collected from the Hopland Research and Extension Center (HREC) in Northern California, which is unceded land of the Shóqowa and Hopland People, on August 28th, 2018 after experiencing mean annual precipitation during the rainy season, see our…

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RdRp scan – identifying/detecting viruses- metagenomic workflow

RdRp scan – identifying/detecting viruses- metagenomic workflow- need help 0 Good afternoon fellow biologists, I have just discovered the joy of bioinformatics on linux (and its frustrations). However, I don’t really understand the workflow for the RdRp scan method to detect viruses. => doi.org/10.1093/ve/veac082 => FIGURE 10 For now: I…

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Coverage of domains

Coverage of domains 0 I have a result file of thousands of sequences from hmmer search of a domain. I want to look at the sequences with best coverage for the domain and want an output that would give me ideally less than 100 seqs with best coverage for the…

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Fetch genomic region(s) from refseq genomes

Fetch genomic region(s) from refseq genomes 2 I would like to fetch specified genomic regions from refseq genomes without having to download the full genome. The regions are previously identified with a hmmer search. To my understandment Ensembl does not have all Refseq genomes. Many thanks, D ensembl • 30…

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Genome-wide analysis and characterization of the LRR-RLK gene family provides insights into anthracnose resistance in common bean

Identification of PvLRR-RLK genes From the kinome of P. vulgaris30, 1203 PKs were identified. Of these, only the proteins endowed with the transmembrane kinase and LRR domains were retained (Supplementary Table S1). All PvLRR-RLKs obtained were analyzed for redundancy following the criterion of maintaining the largest variants in the case…

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(18 August – “Enzyme Stability Prediction”) A free webinar on on-going CAFA5 (Critical Assessment of Functional Annotation of proteins) challenge

Welcome to a webinar: John Mitchell “Kaggle Competition Review: Novozymes Enzyme Stability Prediction” Friday 18 August, 18.00 (CET time, e.g. Paris time) Full announcement: www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/418295 Welcome to the webinar on Friday: John Mitchell who is expert both in bioinformatics and machine learning, and also experienced Kaggler and one of the…

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Genome mining shows that retroviruses are pervasively invading vertebrate genomes

Johnson, W. E. Origins and evolutionary consequences of ancient endogenous retroviruses. Nat. Rev. Microbiol 17, 355–370 (2019). Article  CAS  PubMed  Google Scholar  Stoye, J. P. Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat. Rev. Microbiol 10, 395–406 (2012). Article  CAS  PubMed  Google Scholar  Zheng, J., Wei, Y. &…

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Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle

Bond PL, Hugenholtz P, Keller J, Blackall LL. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol. 1995;61:1910–6. Article  CAS  PubMed  PubMed Central  Google Scholar  Wang Z, Guo F, Liu L, Zhang T. Evidence of carbon fixation pathway in a bacterium from candidate…

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A genome catalogue of lake bacterial diversity and its drivers at continental scale

Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75, 14–49 (2011). Article  CAS  PubMed  PubMed Central  Google Scholar  Pernthaler, J. Competition and niche separation of pelagic bacteria in freshwater habitats….

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(27 July – “DeepLoc”) A free webinar on on-going CAFA5 (Critical Assessment of Functional Annotation of proteins) challenge

Henrik Nielsen,Vineet Thumuluri , José Juan Almagro Armenteros “DeepLoc 2.0: multi-label subcellular localization prediction using protein language models” Thursday 27 July, 19.00 (CET time) Add to Google Calendar The talk will be based on the recent paper with the same title (Nucleic Acids Res. 2022 (www.ncbi.nlm.nih.gov/pmc/articles/PMC9252801/) ). The prediction of…

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What criteria are used to determine significant HMMER hits?

What criteria are used to determine significant HMMER hits? 0 I’m looking at the code here but not very familiar w/ Ruby: github.com/takaram/kofam_scan/blob/master/lib/kofam_scan/result.rb module KofamScan class Result extend Autoload autoload :WithEvalueThreshold autoload :WithThresholdScale autoload :WithThresholdScaleAndEvalueThreshold def self.create(query_list, threshold_scale: nil, e_value_threshold: nil) if threshold_scale && e_value_threshold WithThresholdScaleAndEvalueThreshold.new(query_list, threshold_scale, e_value_threshold) elsif e_value_threshold…

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HMM gets zero or 1 hits when many more expected

HMM gets zero or 1 hits when many more expected 1 Hi all, My ultimate goal is to understand the phylogeny of a set of restriction-modification enzymes among certain genomes. For this, I have done the following: Downloaded all RM genes DNA sequences into psych_rm_genes.fna from REBASE Cleaned rebase file…

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Subject:[QIIME2.2023.5] Need help with Qiime2 installation: ResolvePackageNotFound error – Technical Support

Subject: Need help with Qiime2 installation: ResolvePackageNotFound error Dear Qiime2 Community, I hope this message finds you well. I am currently facing an issue during the installation of Qiime2 and would greatly appreciate your assistance in resolving it. During the installation process, after following the Qiime2 instructions, I encountered the…

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Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group

Isolate storage, growth, and identification Historical BFG isolates originally cultured from clinical material between 1973 and 2018 were stored either lyophilized or frozen in skim milk media at the National Institutes of Health Clinical Center Department of Laboratory Medicine (Bethesda, MD). Isolates were de-identified and metadata including year and source/site…

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Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs

Booth, B. C. & Marchant, H. J. Parmales, a new order of marine chrysophytes, with desriptions of three new genera and seven new species. J. Phycol. 23, 245–260 (1987). Article  Google Scholar  Ichinomiya, M. et al. Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to…

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Prediction of Ribosomal RNA Genes Using RNAmmer Software

Introduction Ribosomal RNA (rRNA) genes are known to be an integral part of ribosome synthesis machinery hence been studied extensively. Due to their repetitive nature, evolutionary converseness, and ubiquitous distribution /omnipresence, these genes are playing a key role in varying functions and mechanisms including maintenance of genome integrity, control of…

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Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors

Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar  Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar  Zetsche, B. et al. Cpf1 is a single…

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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…

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failed to find the gene identifier attribute

featureCounts: ERROR: failed to find the gene identifier attribute 1 Hello I made my own gtf file from hmmer results and I used it to calculate abundance of genes from the annotated feature of my gtf file using featureCounts program. The error message that I got is the following: featureCounts…

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docker – python: can’t open file ‘/home/administrator/alphafold/run_alphafold.py’: [Errno 2] No such file or directory

I’m trying to run docker for alphafold but it says that there is no ‘/home/administrator/alphafold/run_alphafold.py’ in the directory even if it does exist Code I’m trying to run python3 docker/run_docker.py \ –fasta_paths=your_protein.fasta \ –max_template_date=2022-01-01 \ –data_dir=/data8/Alphafold_database\ –output_dir=/data8/Alphafold_output_dir OBS: this is just a test to know if docker is working (your_protein.fasta…

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Prediction of protein subplastid localization and origin with PlastoGram

Data sets To create data sets of sequences corresponding to compartments of photosynthetic plastids, we searched the UniProt database for proteins annotated as localized in the chloroplast. Importantly, the UniProt keyword ’Chloroplast’ includes not only chloroplasts of green algae and land plants but also plastids of Rhodophyta, haptophytes and the…

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Ancient gene linkages support ctenophores as sister to other animals

Ryan, J. F. et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science 342, 1242592 (2013). Article  PubMed  PubMed Central  Google Scholar  Halanych, K. M. The ctenophore lineage is older than sponges? That cannot be right! Or can it? J. Exp. Biol. 218,…

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Error when converting hmmsearch output to gff file

Error when converting hmmsearch output to gff file 0 Hello, I’m trying to convert a hmmsearch output to gff format. For this, I ran the following: hmmsearch –domtblout dom_results.txt –cpu 10 hydrocarbon.hmm orfs_file.faai > demo.log After getting the dom_Results.txt table, I ran the hmmer2gff program from the mgkit program: hmmer2gff…

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error when converting hmmer table to off table

Hello, I performed an alignment using hmmer hmmsearch tool using metagenomic contigs as a query and a hydrocarbon database (hydrocarbon.hmm file). I n first instance I first retrieved all ORFs from the contigs and translated them with esl-translate program as following: esl-translate -c 11 input_contigs.fa > translated_orfs.fa After getting the…

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Unable to create environment – Technical Support

Tried to create an environment using Conda and was not able to do so. Have copy pasted the message below. Would be grateful to know what the issue is and how to resolve the issue. (base) C:\Users\Mathangi Janakiraman>wget data.qiime2.org/distro/core/qiime2-2023.2-py38-linux-conda.yml–2023-05-11 12:54:47– data.qiime2.org/distro/core/qiime2-2023.2-py38-linux-conda.ymlResolving data.qiime2.org (data.qiime2.org)… 54.200.1.12Connecting to data.qiime2.org (data.qiime2.org)|54.200.1.12|:443… connected.ERROR: cannot verify…

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Trying to use hmmer to search genes over metagenome assembled genomes

Trying to use hmmer to search genes over metagenome assembled genomes 0 Hello I have a hmm file (my genes.hmm) that I want to use to search some genes over some MAGs that I elaborated. For this purpose I installed hmmer and tried to run hmmsearch as the following: First…

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Long-Read Metagenomics and CAZyme Discovery

La Rosa SL, Ostrowski MP, Vera-Ponce de León A, McKee LS, Larsbrink J, Eijsink VG, Lowe EC, Martens EC, Pope PB (2022) Glycan processing in gut microbiomes. Curr Opin Microbiol 67:102143. doi.org/10.1016/j.mib.2022.102143 CrossRef  CAS  PubMed  Google Scholar  Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette…

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Scan multiple sequences on multiple hmm profiles

Scan multiple sequences on multiple hmm profiles 1 I want to “align” multiple protein sequences in a multi-fasta file against thousand of hmm profiles (.hmm) that I’ve downloaded. I though on using hmmscan. Should I do that on each profile separately? Or is there a way to work on multiple…

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The Biostar Herald for Monday, April 24, 2023

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…

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Mirusviruses link herpesviruses to giant viruses

Vincent, F., Sheyn, U., Porat, Z., Schatz, D. & Vardi, A. Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise. Proc. Natl Acad. Sci. USA 118, e2021586118 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  Suttle, C. A. Marine viruses — major players in the global…

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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…

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Previously uncharacterized rectangular bacterial structures in the dolphin mouth

To maximize reproducibility, a list of the reagents and resources used in this study, as well as their source and identifier, is provided in Supplementary Table 5. Experimental model and subject details Oral swab samples were obtained from bottlenose dolphins (Tursiops truncatus) managed by the U.S. Navy MMP Biosciences Division, Space…

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RepeatMasker species error

RepeatMasker species error 1 Hi, I am trying to run RepeatMasker with the following command: RepeatMasker –species mammals seq1.fasta But I get the following error: RepeatMasker version 4.1.1 Search Engine: HMMER [ 3.3.2 (Nov 2020) ] Using Master RepeatMasker Database: /Volumes/Seagate/Vasudha/Tools/RepeatMasker/Libraries/RepeatMaskerLib.h5 Title :Version :Date :Families : Species “mammals” is not…

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A male-killing gene encoded by a symbiotic virus of Drosophila

Collection and maintenance of Drosophila biauraria We used laboratory stocks of Drosophila biauraria (Diptera; Drosophilidae), which were originally collected at the Field Science Center for Northern Biosphere, Hokkaido University located at Tomakomai, Hokkaido in 2011 and 2015 using standard banana traps and sweeping22. Females were brought into the lab and…

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Accurate prediction by AlphaFold2 for ligand binding in a reductive dehalogenase and implications for PFAS (per- and polyfluoroalkyl substance) biodegradation

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Baek, M. et al. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 871–876 (2021). Article  ADS  CAS  PubMed  PubMed Central  Google…

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How to fix “Please indicate the file directory in ‘setting’ file?” for MaxBin2?

How to fix “Please indicate the file directory in ‘setting’ file?” for MaxBin2? 1 I can’t figure out why this is happening. I’m running the same command for all of my samples but I’m only getting the error on some. I’ve even found the setting file and put the directories…

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how to iteratively search sequences against sequence database using profile HMM

how to iteratively search sequences against sequence database using profile HMM 1 Hi all, I wonder whether there is a tool for iterative sequence searching using a profile HMM, the task as like the domain construction in Pfam database. jackhmmer can iteratively search sequence against a sequence database, but it…

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Discovery and comparative genomic analysis of a novel equine anellovirus, representing the first complete Mutorquevirus genome

Manzin, A., Mallus, F., Macera, L., Maggi, F. & Blois, S. Global impact of Torque teno virus infection in wild and domesticated animals. J. Infect. Dev. Countries 9, 562–570 (2015). Article  CAS  Google Scholar  Biagini, P. et al. Family Anelloviridae. In Virus Taxonomy: Ninth Report of the International Committee on…

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A bivalent remipede toxin promotes calcium release via ryanodine receptor activation

Recombinant peptide production Recombinant expression of Xt3a, Xt3a-D1, Xt3a-D2 and IpTxA was performed using an E. coli expression system. A gene encoding the peptide was subcloned into an expression vector containing a coding region with poly-histidine purification tag as well as a solubility tag (MBP for Xt3a and SUMO for…

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A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics | Environmental Microbiome

Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F, et al. Insights into the phylogeny and coding potential of microbial dark matter nature. Nat Publ Group. 2013;499:431–7. CAS  Google Scholar  Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, et al. Unusual biology across…

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Co-diversification of an intestinal Mycoplasma and its salmonid host

Alberdi A, Aizpurua O, Bohmann K, Zepeda-Mendoza ML, Gilbert MTP. Do vertebrate gut metagenomes confer rapid ecological adaptation? Trends Ecol Evol 2016;31:689–99. Article  PubMed  Google Scholar  Groussin M, Mazel F, Alm EJ. Co-evolution and co-speciation of host-gut bacteria systems. Cell Host Microbe. 2020;28:12–22. Article  CAS  PubMed  Google Scholar  Alberdi A,…

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Redirecting pHMMER output to /dev/null

Redirecting pHMMER output to /dev/null 2 Hey guys, Something that should be so simple has been so difficult for me to resolve the past few weeks. I am using pHMMER to search my ~12,000 fungal gene predictions against the MEROPS database. The issue is that for some of my gene…

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How To Install clustalw on Ubuntu 20.04

In this tutorial we learn how to install clustalw on Ubuntu 20.04. clustalw is global multiple nucleotide or peptide sequence alignment 633246bd8fd1b951f15985f7cbfb1909 Introduction In this tutorial we learn how to install clustalw on Ubuntu 20.04. What is clustalw clustalw is: This program performs an alignment of multiple nucleotide or amino…

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Issue with hmmcalibrate during tutorial.

Issue with hmmcalibrate during tutorial. 1 Hi everyone. I’m trying to do the tutorial for hmmer but I seem to be having an issue for hmmcalibrate. I tried to use: hmmcalibrate globin.hmm But it says: Command ‘hmmcalibrate’ not found, did you mean: command ‘hmm2calibrate’ from deb hmmer2 (2.3.2+dfsg-6) Try: sudo…

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Phylogenetic and AlphaFold predicted structure analyses provide insights for A1 aspartic protease family classification in Arabidopsis

Introduction Proteases regulate various biological processes including protein synthesis and maturation, activity modification, degradation and turnover. Depending on their catalytic mechanisms, these proteases are primarily classified into cysteine, metallo-, serine, threonine and aspartic protease family (Beers et al., 2004). The latter protease family is known as acid protease family because they…

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issues with amber_minimize.py failing to use CUDA within alphafold

issues with amber_minimize.py failing to use CUDA within alphafold 0 When I try and run alphafold from ubuntu command line with amber enabled, it’s throwing these errors. I0125 17:33:14.174568 47215575258112 amber_minimize.py:407] Minimizing protein, attempt 1 of 100. I0125 17:33:14.555528 47215575258112 amber_minimize.py:68] Restraining 685 / 1336 particles. I0125 17:33:14.747518 47215575258112 amber_minimize.py:417]…

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Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps

Genomic features of two Anastatus wasps, A. japonicus and A. fulloi We employed PacBio high-fidelity (HiFi) long-read sequencing and Illumina short-read sequencing technologies to generate high-quality contigs for two Anastatus wasps, A. japonicus and A. fulloi (Supplementary Tables 1 and 2). These contigs were further scaffolded using Hi-C libraries to…

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Bioinformatics Research Scientist (Blue Sky Initiative), Memphis, Tennessee

M. Madan Babus Group and the Center for Data-Driven Discovery in the Department of Structural Biology is seeking a highly driven, Full time Machine Learning Research Scientist support the Kalodimos and Babu Groups on the Blue Sky Initiative “Seeing the Invisible in Protein Kinases.” This project is supported by $35…

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Petabase-scale sequence alignment catalyses viral discovery

Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…

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ncRNA | Free Full-Text | Common Features in lncRNA Annotation and Classification: A Survey

CONC 2006 SVM Eukaryotes (both protein-coding and non-coding genes) peptide length, amino acid composition, predicted secondary structure content, mean hydrophobicity, percentage of residues exposed to solvent, sequence compositional entropy, number of homologues, alignment entropy 10-fold CV on protein-coding: F1-score: 97.4% ☼ Precision: 97.1% ☼ Recall: 97.8% ◙ On non-coding: F1-score:…

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alphafold2: HHblits failed – githubmemory

I’ve tried using the standard alphafold2 setup via docker (converted to a singularity container) via the setup described at github.com/kalininalab/alphafold_non_docker, and both result in the following error: […] E1210 12:01:01.009660 22603932526400 hhblits.py:141] – 11:49:18.512 INFO: Iteration 1 E1210 12:01:01.009703 22603932526400 hhblits.py:141] – 11:49:19.070 INFO: Prefiltering database E1210 12:01:01.009746 22603932526400 hhblits.py:141]…

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Issue with installing QIIME2 2021.11 on Windows 10 – Technical Support

Hi QIIME support team, I’m attempting to install QIIME2 on my Windows 10 machine. I installed Anaconda3, then set up conda to run in Git Bash: echo “. ${PWD}/conda.sh” >> ~/.bashrc Once I restarted Git Bash and activated Conda, I installed python-wget because installation of wget kept getting the following…

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Install alphafold on the local machine, get out of docker.

AlphaFold This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document. Any publication that discloses findings arising from…

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alphafold colab github

for the third time worked! Found inside – Page iiThe eight-volume set comprising LNCS volumes 9905-9912 constitutes the refereed proceedings of the 14th European Conference on Computer Vision, ECCV 2016, held in Amsterdam, The Netherlands, in October 2016. Please make sure you have a large enough hard drive space, bandwidth…

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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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Comment: alphafold online availability and use case

Not my area of expertise particularly but; 1. I don’t think you can use a structure prediction tool to really ‘validate’ HMMER predictions. I’m pretty sure most structure predictors are relying on HMMER or similar HMM based approaches (Martin told me AlphaFold leans on HHBlits API calls for example). I…

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alphafold online availability and use case

I’m new to both protein structure prediction and the use of AI-based tools like Alphafold2 or RoseTTAFold. And I have a few questions: **1.** Is it possible to use structure prediction by AlphaFold2 to **validate** HMMER based domain sequence predictions? If yes, what would be the steps? I have some…

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Help speeding up HMMER’s HMMSearch algorithm for large fasta file with GNU Parallel

I’ve seen that HMMER can be sped up with GNU Parallel: Speed of hmmsearch I have around 100,000 sequences and a HMMER database of around 300 HMM profiles. I’m running everything at once but I’m wondering if it’ll be faster to split up the sequences and/or split up the jobs….

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