Tag: HMM

Time-independent variation is present in 16S GCN evolution To evaluate the extent of time-independent or intraspecific variation in 16S GCN, we examined 5437 pairs of genomes with identical 16S rRNA gene alignments. The 16S GCN differs in 607 (11%) of them, suggesting the presence of significant time-independent variation. For the…

Dargie, G. C. et al. Age, extent and carbon storage of the central Congo Basin peatland complex. Nature 542, 86–90 (2017). Article  ADS  CAS  PubMed  Google Scholar  Page, S. E., Rieley, J. O. & Banks, C. J. Global and regional importance of the tropical peatland carbon pool. Global Change Biology…

Unraveling the Mysteries of Hidden Markov Models: A Deep Dive into Sequential Data Analysis Hidden Markov Models (HMMs) have become an essential tool in the world of data analysis, particularly when it comes to analyzing sequential data. These models have been widely used in various fields, including finance, speech…

Exploring the Viterbi Algorithm: Decoding Hidden Markov Models for Optimal Sequence Prediction The Viterbi Algorithm, named after its inventor Andrew Viterbi, is a powerful tool for unveiling the most likely sequence of hidden states in a Hidden Markov Model (HMM). This dynamic programming algorithm has found numerous applications in…

Johnson, W. E. Endogenous retroviruses in the genomics era. Annu. Rev. Virol. 2, 135–159 (2015). Article  CAS  PubMed  Google Scholar  Johnson, W. E. Origins and evolutionary consequences of ancient endogenous retroviruses. Nat. Rev. Microbiol. 17, 355–370 (2019). Article  CAS  PubMed  Google Scholar  Johnson, W. E. Endless forms most viral. PLoS…

Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995;59:143–69. CAS  PubMed  PubMed Central  Google Scholar  Konstantinidis K, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J. 2017;11:2399–406. PubMed  PubMed Central  Google Scholar  Parks…

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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…

Mandáková, T. & Lysak, M. A. Post-polyploid diploidization and diversification through dysploid changes. Curr. Opin. Plant Biol. 42, 55–65 (2018). Article  PubMed  Google Scholar  Blanc, G. & Wolfe, K. H. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16, 1667–1678 (2004). Article  CAS …

I’m working with matched single cell data, where we have treated and untreated samples for the same patient. I ran CNV analysis using the infercnv package. I’ve followed the tutorial: # data matrix counts_matrix <- scData@assays$RNA@counts meta = data.frame(labels = Idents(scData), row.names = names(Idents(scData))) unique(meta$labels) # check the cell labels…

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….

Some mitochondrial mRNA are circularized CircTAIL-seq is a technique used to Illumina sequence individual transcript PCR libraries of mitochondrial mRNA tails. The approach captures enough of each molecule’s 5′ and 3′ termini that the presence of editing can be confirmed if necessary17. Library preparation first requires circularizing total RNA with…

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…

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…

HMSS2: an advanced tool for the analysis of sulfur metabolism, including organosulfur compound transformation, in genome and metagenome assemblies Abstract The global sulfur cycle has implications for human health, climate change, biogeochemistry, and bioremediation. The organosulfur compounds that participate in this cycle not only represent a vast reservoir of sulfur,…

Dick G, Anantharaman K, Baker B, Li M, Reed D, Sheik C. The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats. Front Microbiol. 2013;4:124. Dick GJ. The microbiomes of deep-sea hydrothermal vents: distributed globally, shaped locally. Nat Rev Microbiol. 2019;17:271–83. Article  CAS …

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…

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…

I extracted three samples (HG02024 – HG02026) from the 1000 Genomes Project’s 30x alignment files, employing the Genome Analysis Toolkit (GATK) best practice pipeline. This process involved performing base quality score recalibration, identifying and removing duplicate reads, utilizing the HaplotypeCaller to generate a genomic VCF (gVCF) file, and calling variants…

Hi, I call gvcf file using GATK HaplotypeCaller as following: gatk HaplotypeCaller -R my.fasta \ -I s-95.sort.noDup.bam \ -L 3R:23000000-27905053 \ -ERC GVCF \ -bamout test_s95.bamout.bam \ –native-pair-hmm-threads 28 \ -O test_s95.sort.noDup.g.vcf The above ouput gvcf reports a variant at 3R:25063300 3R 25063300 . C T,<NON_REF> 804.64 . BaseQRankSum=-2.060;DP=59;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=212400,59;ReadPosRankSum=-1.269 GT:AD:DP:GQ:PGT:PID:PL:PS:SB…

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…

Whitman, W. B., Coleman, D. C. & Wiebe, W. J. Prokaryotes: the unseen majority. Proc. Natl Acad. Sci. USA 95, 6578–6583 (1998). Article  CAS  PubMed  PubMed Central  Google Scholar  Herndl, G. J. & Reinthaler, T. Microbial control of the dark end of the biological pump. Nat. Geosci. 6, 718–724 (2013)….

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…

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….

how to make a header name in a haplotyping script of gatk? 1 Hi, I want to ask how we can make the header name as per our choice in a haplotyping script of gatk because by default the header name of the output.vcf file is mentioned as sample1? here…

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 …

Suttle, C. A. Environmental microbiology: Viral diversity on the global stage. Nat. Microbiol. 1, 16205 (2016). Article  CAS  PubMed  Google Scholar  Schulz, F. et al. Giant virus diversity and host interactions through global metagenomics. Nature 578, 432–436 (2020). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Dutilh, B. E., Reyes,…

I want to simulate variant calling of an ultra-low-coverage >0.005x bam file. I subsampled reads from the (HG02024) sample of the 1KG phase 3 dataset. My code in R to do so is the following (bam and reference are just path extensions, file is the inital bam file): cov_rate <-…

Joye, S. B. The geology and biogeochemistry of hydrocarbon seeps. Annu. Rev. Earth Planet. Sci. 48, 205–231 (2020). Article  CAS  Google Scholar  Feng, D. et al. Cold seep systems in the South China Sea: An overview. J. Asian Earth SCI 168, 3–16 (2018). Article  Google Scholar  Dubilier, N., Bergin, C….

I’m attempting to do a strainphlan analysis of Blautia wexlerae, but nothing I’m doing is working. I think the problem might be the reference genomes that I’m using, but I’m using the 2 primary genomes from NCBI. Is there another place to get correctly formatted references? Error Here’s the primary…

Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007). Article  CAS  PubMed  PubMed Central  Google Scholar  Glöckner, J. et al. Phylogenetic diversity and metagenomics of candidate division OP3. Environ. Microbiol. 12, 1218–1229…

I would like to extract the physically phased haplotypes from a VCF file generated by GATK’s HaplotypeCaller on Illumina data of some isolates from different yeast (S. cerevisiae) strains. According to this FAQ: In the format field of a PGT (Pre-Implantation Genetic Testing) VCF, you may find a description similar…

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…

MERVL exhibits distinct localization in mouse embryos To understand the dynamics of MERVL expression, we first analyzed publicly available single-cell RNA-sequencing (scRNA-seq) datasets from each blastomere at eight representative stages of preimplantation development18 (Fig. 1a). To define regions of nonredundant MERVLs in mouse genome, we used RepeatMasker to annotate the…

Moore CM, Mills MM, Arrigo KR, Berman-Frank I, Bopp L, Boyd PW, et al. Processes and patterns of oceanic nutrient limitation. Nat Geosci. 2013;6:701–10. Article  CAS  Google Scholar  Sohm JA, Webb EA, Capone DG. Emerging patterns of marine nitrogen fixation. Nat Rev Microbiol. 2011;9:499–508. Article  CAS  PubMed  Google Scholar  Zehr…

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…

Zhang J, Liu Y, Zhang N, Hu B, Jin T, Xu H, et al. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nat Biotechnol. 2019;37:676–84. Article  CAS  PubMed  Google Scholar  Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. Going back to the roots:…

GATK showing error of reference file index 0 Hi, i am using the GATK version gatk/4.2.2.0 for HaplotypeCaller. I have been facing the reference.fa indexing issue. I tried to index the file using the following command samtools faidx ~/path/PitayaGenomic.fa #three difference formats of reference files -rw-r–r– 1 tariqr 1.3G Feb…

Our metazoan-wide survey has provided the most comprehensive analysis to date of gene number and phylogenetic distribution of three key antioxidant gene families across the animal kingdom. Genes encoding all three families were observed in 18 metazoan species; the exception is the ctenophore Mnemiopsis leidyi that has PRX and GPX,…

Animal studies Animal care and study protocols were approved by the AAALAC-accredited Institutional Animal Care and Use Committee of the College of Agricultural Life Sciences at the University of Wisconsin-Madison (UW-Madison). All experiments with mice were performed under protocols approved by the UW-Madison Animal Care and Use Committee (Protocol number…

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…

Proportion of AlphaFold2 models that can be brought into CATH Identification of domains in AF2 protein models We applied an in-house Hidden-Markov Model-based protocol CATH-Resolve-Hits (CRH)26 to assign domain regions in all sequences from the 21 model organisms modelled by AlphaFold2 (AF2) (see “Methods” for description and Fig. 1). CRH identifies…

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…

Orcutt B, D’Angelo T, Jungbluth SP, Huber JA, Sylvan JB. Microbial life in oceanic crust. OSF Preprints, 2020; doi.org/10.31219/osf.io/2wxe6. Koonin EV. On the origin of cells and viruses: primordial virus world scenario. Ann NY Acad Sci. 2009;1178:47–64. Nigro OD, Jungbluth SP, Lin HT, Hsieh CC, Miranda JA, Schvarcz CR, et…

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…

Faking hh-suite workflow / alignment output 1 Given the following: query.fasta -> single entry reference.fasta -> multiple entries I now want to ‘fake’ (or just be able to get) an output that looks like a proper *.hhr alignment file, i.e. as if I aligned the query.fasta against the profiles of…

A paralog of Pcc1 is widely distributed among archaea The recent discovery of a fifth subunit of KEOPS in metazoa raised the possibility that a corresponding subunit could exist in archaea. In search for such a subunit, we noticed in the model archaeon Thermococcus kodakarensis KOD1 the existence of two…

Hello everybody, I am using pharmcat tool’s prerprocessor feature to preprocessmy vcf file using the command > python3 pharmcat_vcf_preprocessor.py -vcf sample.vcf But I think there is some issue with my vcf file as this command outputs an error > Reading samples from sample.vcf … Saving output to . > >…

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TCR sequence analysis 2 Hi, I’m doing single-cell TCR sequencing using Mark Davis’ protocol. Here is the link to Davis paper: www.nature.com/nbt/journal/v32/n7/abs/nbt.2938.html The paper used vdjfasta for TCR analysis. But the vdjfasta was set up for antibody sequence analysis. When I use it for TCR sequences, I don’t get exactly…

Development of the CusProSe software CustomProteinSearch (CusProSe) is a generic genome mining software, consisting of two distinct but complementary customizable programs: IterHMMBuild and ProSeCDA. IterHMMBuild is an HMM profile building tool based on an iterative learning process. ProSeCDA is a protein search and annotation tool based on user-defined domain architectures….

Hmm, I am assuming that since you are referring to canidae then you want “family level” information. I know you can do this bioinformaticly by getting a large list of different species that are also from different genus (one taxa from each known species /genus). Add in a few taxa…

Scatter Gather principle by chromosome on Gatk 0 Hi all, On a quest to optimize gatk pipeline, I met scatter gather principle, so I did following, pids= for chr in chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20…

Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048. Article  PubMed  Google Scholar  Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, et al. Genomic expansion of domain archaea highlights roles…

Miyakawa, T., Matsuzawa, H., Matsuhashi, M. & Sugino, Y. Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis. J. Bacteriol. 112, 950–958 (1972). Article  CAS  PubMed  PubMed Central  Google Scholar  Ayala, J. A., Garrido, T., De Pedro,…

Visualization of Pool-HMM results 0 Hello everyone, I have run the Pool-HMM tool on my pool-seq data and got final results in this format Chr Start End Pool-HMM 1 312212 413291 11.60071199 1 595314 676207 11.40558651 1 3136358 3180593 11.65338609 1 3788166 3813896 4.561544648 1 5202297 5218014 1.620942559 1 5448808…

Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924). Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol….

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.,…

Subjects Normal breast and tumor samples were obtained with the written informed consent from donors and appropriate approval from local ethical committees, with the detailed information described in the respective original publications: normal tissue9, METABRIC14, TCGA35. Differential allelic expression analysis DNA and total RNA from 64 samples of normal breast…

Pytorch Seq2seq Tutorials on implementing a few sequence-to-sequence (seq2seq) models with PyTorch and TorchText. Rnn ctc Recurrent Neural Network and Long Short Term Memory (LSTM) with Connectionist Temporal Classification implemented in Theano. Includes a Toy training example. Haste Haste: a fast, simple, and open RNN library Eeg Dl A Deep…

Sequencing data We used publicly available sequencing data from the GIAB consortium45, 1000 Genomes Project high-coverage data46 and Human Genome Structural Variation Consortium (HGSVC)4. All datasets include only samples consented for public dissemination of the full genomes. Statistics and reproducibility For generating the assemblies, we used all 14 samples for…

Bio::Search::HSP::WABAHSP(3) HSP object suitable for describing WABA alignments SYNOPSIS # use this object as you would a GenericHSP # a few other methods have been added including state DESCRIPTION This object implements a few of the extra methods such as hmmstate_string which returns the HMM state representation for the WABA…

Hmm 0 views I like this I dislike this Related questions What do u mean by hug? Why is hidden Markov used in speech recognition? What is profile in bioinformatics? What is HMM in bioinformatics? What is hidden Markov in speech recognition? What is hmm called? What Mmmm means? What…

NCBI HMM accession Source identifier Product name Label Gene symbol Family type EC number(s) GO term(s) HMM length Sequence cutoff Domain cutoff Number of RefSeq protein hits counting … HMM profile HMM seed Named by this model (…) Other hits (…) No RefSeq protein is named by this evidence. Failed…

I am trying to use the -L option of GATK HaplotypeCaller to call SNPs and short InDels with in an interval list. My interval list file (top8snp.interval_list) content is as follows: 12 33029845 33030845 + rs24767598 13 40586682 40587682 + rs24748362 18 24373857 24374857 + rs8856159 21 50381146 50382146 +…

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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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]…

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…

LOCUS NC_002528 640681 bp DNA circular BCT 07-JUN-2007 DEFINITION Buchnera aphidicola str. APS (Acyrthosiphon pisum), complete genome. ACCESSION NC_002528 VERSION NC_002528.1 GI:15616630 KEYWORDS . SOURCE Buchnera aphidicola str. APS (Acyrthosiphon pisum) ORGANISM Buchnera aphidicola str. APS (Acyrthosiphon pisum) Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Buchnera. REFERENCE 1 (sites) AUTHORS Shigenobu,S., Watanabe,H.,…

Significance CRISPR-Cas12a has emerged as attractive molecular scissors alternative to Cas9 owing to its unique features including fewer off-target effects, an alternative protospacer-adjacent motif sequence, pre-CRISPR RNA processing activity, and indiscriminate single-stranded DNase activity. However, despite these advantages, Cas12a has not been well utilized as recently reported base and prime…

Snakemake: MissingInputException 0 Hello, I am trying to create a simple Snakemake workflow and I am having some issues. My file looks like this: ——————– ARCHIVE_FILE = ‘output.tar.gz’ **a single output file** OUTPUT_FILE = ‘output/{species}.out’ **a single input file** INPUT_FILE = ‘proteins/{species}.fasta’ **Build the list of input files.** INP =…

1. Latgé, J. P. and Chamilos, G. Aspergillus fumigatus and Aspergillosis in 2019. Clin. Microbiol. Rev. doi.org/10.1128/CMR.00140-18 (2019). 2. Invasive Aspergillosis. LIFE www.life-worldwide.org/fungal-diseases/invasive-aspergillosis (2020). 3. Harrison, N. et al. Incidence and characteristics of invasive fungal diseases in allogeneic hematopoietic stem cell transplant recipients: a retrospective cohort study. BMC Infect. Dis….

Source: minimac4 Version: 1.0.2-3 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of minimac4 the autopkgtest of minimac4 fails in testing when that autopkgtest is run with the binary packages of minimac4 from unstable. It passes when run with only packages from testing. In…

A library of tested, GPU implementations of core structured prediction algorithms for deep learning applications. HMM / LinearChain-CRF HSMM / SemiMarkov-CRF Dependency Tree-CRF PCFG Binary Tree-CRF … Designed to be used as efficient batched layers in other PyTorch code. Tutorial paper describing methodology. Getting Started !pip install -qU git+https://github.com/harvardnlp/pytorch-struct #…

Name Last modified Size Description Parent Directory   –   Affy/ 2014-05-29 05:25 –   Align/ 2014-06-11 10:27 –   AlignIO/ 2014-06-11 10:27 –   Alphabet/ 2014-06-11 10:27 –   Application/ 2014-05-29 05:25 –   Blast/ 2014-05-29 05:25 –   CAPS/ 2014-05-29 05:25 –   Cluster/ 2014-05-29 05:25 –  …

(PDF) Predicting MoRFs in protein sequences using HMM profiles | Shiu Kumar – Academia.edu Academia.edu no longer supports Internet Explorer. To browse Academia.edu and the wider internet faster and more securely, please take a few seconds to upgrade your browser. Academia.edu uses cookies to personalize content, tailor ads and improve the…

How to use output from GeneMark-ES to identify function? 2 Hello everyone, I would like to ask anyone who know about How to use result from GeneMark-ES program to identify function? For now I already have a result like below of this post. And It’s include Nucleotide sequences output but…

1. Strassert, J. F. H., Irisarri, I., Williams, T. A. & Burki, F. A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids. Nat. Commun. 12, 1879 (2021). ADS  CAS  PubMed  PubMed Central  Google Scholar  2. Burki, F., Roger, A. J., Brown, M. W. &…

This question was migrated from Unix & Linux Stack Exchange because it can be answered on Bioinformatics Stack Exchange. Migrated 8 hours ago. I am trying to extract the protein sequence of specific genes from gene bank like format file obtained from antismash part of which looks like…

Hello everyone, I used this program called antismash to predict the secondary metabolite clusters in my genome of interest. The output I got is gene bank like format whish is shown below: LOCUS scaffold_10 47160 bp DNA linear UNK 01-JAN-1980 DEFINITION scaffold_10. ACCESSION scaffold_10 VERSION scaffold_10 KEYWORDS . SOURCE ORGANISM…

Annotation tools (prokaryotes): prokka vs eggnog 1 Are there any obvious advantages/disadvantages to using one over the other? Both use HMM (I think), both are hierarchical (starting with EggNOG 4.5). Are they simply competitors? Perhaps there is a trade-off between database size (Prokka is smaller) and the quality of curation?…

1. Pérez, J., Moraleda-Muñoz, A., Marcos-Torres, F. J. & Muñoz-Dorado, J. Bacterial predation: 75 years and counting!. Environ. Microbiol. 18, 766–779 (2016). PubMed  Article  PubMed Central  Google Scholar  2. Linares-Otoya, L. et al. Diversity and antimicrobial potential of predatory bacteria from the Peruvian coastline. Mar. Drugs. 15, E308. doi.org/10.3390/md15100308 (2017)….

Update protein annotation on databases 1 Hello all, I’m a bit new to the computational biology scene, and I would like information regarding how protein annotations are curated and how individuals can submit protein annotations. I ask because my team and I recently published a paper that shows the function…

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

How to train annotations tools 1 I would like to train Augustus, SNAP and GlimmerHMM. I found protein sequences in GenBank and in orthodb.org. Furthermore, I found HMM files on busco-data.ezlab.org. $ wget -c busco-data.ezlab.org/v5/data/lineages/viridiplantae_odb10.2020-09-10.tar.gz $ wget -c v100.orthodb.org/download/odb10_plants_fasta.tar.gz Are there any instructions on how to train those annotations tools?…

    This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see ADaCGH2. Analysis of data from aCGH experiments using parallel computing and ff objects Bioconductor version: 2.12 Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as…

GATK mutech2: Sample not found in BAM header 0 I get the following error when running mutech2, any idea what the reason is: A USER ERROR has occurred: Bad input: Sample N-PANCNGS-006 is not in BAM header: [] gatk Mutect2 –native-pair-hmm-threads 30 -R ~/genomes/BWA/Homo_sapiens.GRCh38.dna.primary_assembly.fa -I T-PANCNGS-006.bam -I N-PANCNGS-006.bam -normal N-PANCNGS-006…

❯ plink1.9 –homozyg –help PLINK v1.90b6.22 64-bit (3 Nov 2020) www.cog-genomics.org/plink/1.9/ (C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3 –help present, ignoring other flags. –homozyg [{group | group-verbose}] [‘consensus-match’] [‘extend’] [‘subtract-1-from-lengths’] –homozyg-snp <min var count> –homozyg-kb <min length> –homozyg-density <max inverse density (kb/var)> –homozyg-gap <max internal gap…

Prokka Annotation or NCBI Annotation 1 Dear All, I have two sets of annotation files for 15 Bacterial genomes. One set from NCBI annotations (from RefSeq) and the other from Prokka (I have run it in my local machine). Which one is advisable to use between the two for all…

I’m trying to add several mult-HMM files together but I haven’t had much luck. First I tried to just cat them, then I realized that it won’t work if there is an overlap of HMMs within the files. I then made a script that only concatenates unique ones but once…

RNAmmer running 1 Dear, I am Kishor from Shanghai. Recently I have been trying to use RNAmmer. But yet to successfully run it. I have made two changes in the rnammer according to instructions, like as follows: my $INSTALL_PATH = “/mnt/genome3/Lab_Users/Kishor/DISK_2/softwares/RNAmmer” **for linux HMMSEARCHBINARY=”/mnt/genome3/LabUsers/Kishor/DISK2/softwares/hmmer2/hmmer−2.3.2/src/” $PERL = “/usr/bin/perl” I also changed…

IMPUTE2 – problem with MCMC 1 Dear, I’ve run an imputation using the fallowing command Impute -use_prephased_g -known_haps_g output_phased.haps -h 1000GP_Phase3.hap.gz -l 1000GP_Phase3.legend.gz -m genetic_map.txt -int 1 1000000 -iter 30 -o Part1_impute I do not understand why the MCMC iteration are not 30, but 1. (see output) —————- Run parameters…

28 set blast protein alignment Posted at 20:44h in Sem categoria by BLAST applied the standard genetic code for Query, translating GTG into valine (V). The BLAST is a set of algorithms that attempt to find a short fragment of a query sequence that aligns perfectly with a fragment of…

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bad file format in HMM file 1 Hi people, I am trying to run hmmpress hmmpress ./data/dbCAN-HMMdb-V8.txt But i have the following error: Working… bad file format in HMM file data/dbCAN-HMMdb-V8.txt Please, help me, Thanks hmmpress hmmer • 29 views A file ending in .txt may not be a HMM…

BLAST versus HMM search 0 Can someone please provide (1) definition of BLAST and HMM searches and (2) describe/explain what the difference is between BLAST and HMM search? PS. This is NOT a homework help. I am trying to understand the concepts behind BLAST and HMM. Thanks in advance! python…