Tag: HMM

Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed  Google Scholar  2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed  PubMed Central  Google Scholar  3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….

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Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). 2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018). CAS  PubMed  Google Scholar  3. Oh, J. et al. Temporal stability…

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Towards the biogeography of prokaryotic genes

1. Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015). PubMed  Google Scholar  2. Zou, Y. et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat. Biotechnol. 37, 179–185 (2019). CAS  PubMed  PubMed Central  Google Scholar  3. Mohammad,…

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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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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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NC 002528 | Virtual Laboratory Wiki

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.,…

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Mg2+-dependent conformational rearrangements of CRISPR-Cas12a R-loop complex are mandatory for complete double-stranded DNA cleavage

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…

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Snakemake: MissingInputException

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 =…

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Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection

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….

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minimac4: autopkgtest regression: *** stack smashing detected ***: terminated

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…

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simonsvaerd/pytorch-struct – Giters

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 #…

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Index of /~psgendb/local/biopython-1.64.old/Bio

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 –  …

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(PDF) Predicting MoRFs in protein sequences using HMM profiles | Shiu Kumar

(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…

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How to use output from GeneMark-ES to identify function?

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…

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Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae

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. &…

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python – Error while parsing gene bank file using Biopython

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…

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How to extract protein sequence of selected genes from gene bank like format

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…

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Annotation tools (prokaryotes): prokka vs eggnog

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?…

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Venatorbacter cucullus gen. nov sp. nov a novel bacterial predator

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)….

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Update protein annotation on databases

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…

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Bioconductor – Bioconductor 3.14 Released

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,…

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How to train annotations tools

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?…

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Bioconductor – ADaCGH2

    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…

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Sample not found in BAM header

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…

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Runs of homozygosity in Plink

❯ 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…

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Prokka Annotation or NCBI Annotation

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…

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How to merge HMM files for HMMSearch?

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…

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RNAmmer running

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…

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IMPUTE2 – problem with MCMC

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…

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blast protein alignment

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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Dice Bioinformatics Engineer Vacancy 2021

Dice Bioinformatics Engineer Vacancy 2021 – Candidates Apply Online Job Title: Bioinformatics Engineer Vertical: Pharmaceutical Address City: San Diego, CA Country: US Position starting out 100% remote due to COVID-19. Anticipated duties. Work closely with world-class scientists, bioinformaticians, and developers to advance the discovery of new biologic medicine. Develop and…

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bad file format in HMM file

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…

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BLAST versus HMM search

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…

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Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)

1. Szathmáry E, Smith JM. The major evolutionary transitions. Nature 1995;374:227–32. PubMed  Google Scholar  2. West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci USA. 2015;112:10112–9. CAS  PubMed  PubMed Central  Google Scholar  3. Moran NA. The coevolution of bacterial endosymbionts and phloem-feeding…

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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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How are the HMM cutoff scores in TIGRFAMs determined?

How are the HMM cutoff scores in TIGRFAMs determined? 0 Hello everyone, As indicated in the title, I am wondering how are the HMM cutoff scores in TIGRFAMs determined? Where did I find the score? (If you search a TIGRFAM accession in the NCBI protein family model database, e.g. TIGR02064.1,…

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Can HMMs detect partial proteins sequences?

Can HMMs detect partial proteins sequences? 0 Hello everyone, I am trying to determine the abundance of a gene in a set of metagenomic short reads using the hmm of this gene, then use this method to compare the abundance of the gene across several samples after normalizing for data…

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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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MAKER genome annotation error with SNAP ab initio prediction

I am trying to do a second round of maker genome annotation with ab initio prediction by snap. The error I am getting is as follows: error: unknown command “genome.hmm”, see ‘snap help’. ERROR: Snap failed –> rank=NA, hostname=bioinformatics ERROR: Failed while preparing ab-inits ERROR: Chunk failed at level:0, tier_type:2…

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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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So many variants detected.

So many variants detected. 0 Dear All, I have done variant calling in Germline data that has single sample of each individual and two genes. I did following steps, but after checking results I found too many variants. After Haplotypecaller (the step 6) I found 140900 known variants, and the…

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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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