Category: HMM

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?…

Continue Reading Annotation tools (prokaryotes): prokka vs eggnog

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)….

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

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…

Continue Reading Update protein annotation on databases

COSMIC prediction

COSMIC prediction 0 Hello everyone, I need to control the FATHMM prediction score for a very long list of mutations. I have the COSMIC IDs for each variant but inserting them on the website by hand takes me too much time. Do you know any better way? Thanks mutation FATHMM…

Continue Reading COSMIC prediction

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,…

Continue Reading Bioconductor – Bioconductor 3.14 Released

GGA lecture 20 – PCR and DNA sequencing – Genes and Gene Action 2 –

GGA lecture 20 – PCR and DNA sequencing – Genes and Gene Action 2 – – StuDocu Home My Library You don’t have any modules yet. You don’t have any books yet. You don’t have any Studylists yet. You haven’t viewed any documents yet. Discovery Read more here: Source link

Continue Reading GGA lecture 20 – PCR and DNA sequencing – Genes and Gene Action 2 –

Removing indels +/- a buffer area? How? : bioinformatics

Hey everyone. Hopefully an easy question but my Googling and looking for papers hasn’t really come up with much. I am using a software (IBDMix) to analyze some Neanderthal DNA vs. Modern humans using the new HG38 1000 Genomes data from earlier this year. The method in the IBDMix paper…

Continue Reading Removing indels +/- a buffer area? How? : bioinformatics

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?…

Continue Reading How to train annotations tools

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…

Continue Reading Bioconductor – ADaCGH2

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…

Continue Reading Sample not found in BAM header

Physics gun in car : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading Physics gun in car : gmod

Kaggle Docker with GPU? : kaggle

Search within r/kaggle Read more here: Source link

Continue Reading Kaggle Docker with GPU? : kaggle

This. : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading This. : gmod

Severe trauma and burns accompanied by sepsis

Introduction Trauma accounts for approximately 10% of deaths and 16% of disabilities worldwide.1 Billions of dollars have been spent on research into new biological therapeutics for severe injuries, as well as post-traumatic sepsis and septic shock.2 Burn injuries cause unpredictable trauma and sepsis is a complication associated with high morbidity…

Continue Reading Severe trauma and burns accompanied by sepsis

Meet a CRISPR crop scientist on World CRISPR Day

Happy World CRISPR Day!  Meet Nicholas Karavolias, a Ph.D. candidate at the University of California, Berkeley in the Plant and Microbial Biology Department. He works at the Innovative Genomics Institute where he uses CRISPR/Cas in his research. What excites you about CRISPR?  So many things! I think CRISPR/Cas technology gives…

Continue Reading Meet a CRISPR crop scientist on World CRISPR Day

Clinical Data from Editas Medicine’s Ongoing Phase 1/2 BRILLIANCE Clinical Trial of EDIT-101 … | News

CAMBRIDGE, Mass., Oct. 20, 2021 (GLOBE NEWSWIRE) — Editas Medicine, Inc. (Nasdaq: EDIT), a leading genome editing company, today announced that an abstract featuring initial clinical data from the BRILLIANCE clinical trial of EDIT-101 has been selected for an oral presentation at the 2021 European Society of Gene and Cell Therapy…

Continue Reading Clinical Data from Editas Medicine’s Ongoing Phase 1/2 BRILLIANCE Clinical Trial of EDIT-101 … | News

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…

Continue Reading Runs of homozygosity in Plink

H20 AutoML : kaggle

Search within r/kaggle Read more here: Source link

Continue Reading H20 AutoML : kaggle

Bullsquid game : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading Bullsquid game : gmod

replica tool gun : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading replica tool gun : gmod

Sexy Gordon Freeman poster. : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading Sexy Gordon Freeman poster. : gmod

Errors : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading Errors : gmod

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…

Continue Reading Prokka Annotation or NCBI Annotation

error in metagenemark

error in metagenemark 0 I have install the metagenemark on linux64, and I have done cp gm_key ~/.gm_key. It still have a error when run the shell. And I search online didn’t find the similar situation. The shell codes is: gmhmmp -m MetaGeneMark_v1.mod -a -k -f G -o gene.gff ./04_metaSPAdes/contigs.fasta…

Continue Reading error in metagenemark

GO BACK TO WORK!! : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading GO BACK TO WORK!! : gmod

Gmod Recon Soldier Art : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading Gmod Recon Soldier Art : gmod

Collapse overlapping annotations in R

I am trying to use the R package groHMM to analyse some data and it wants me to Collapse overlapping annotations but I am working with Arabidopsis and not human data. groHMM uses the R package GenomicFeatures for annotations. I am using TxDb.Athaliana.BioMart.plantsmart28 but the tool wants me to collapse…

Continue Reading Collapse overlapping annotations in R

Help with TMHMM

Help with TMHMM 0 Hi people! I’m trying install TMHMM in my computer (ubuntu 18.04), but I have some error when run tmhmm this error: (base) iim-unah@iimunah-Precision-7820-Tower:~/tools/tmhmm/bin$ ./tmhmm seq.fasta syntax error at ./tmhmm line 13, near “$opt_basedir:” Unknown regexp modifier “/t” at ./tmhmm line 13, at end of line Unknown…

Continue Reading Help with TMHMM

Florida Dark RP Gmod : BrandNewSentence

Search within r/BrandNewSentence r/BrandNewSentence Read more here: Source link

Continue Reading Florida Dark RP Gmod : BrandNewSentence

Set a %coverage threshold during a hmmsearch using HMMer

Set a %coverage threshold during a hmmsearch using HMMer 1 Hi everyone, I would like to know if there is a way to set a %coverage treshold using hmmsearch. I’ve read the user guide, but i haven’t found it.   Regards, C. sequence • 2.4k views • link updated 2…

Continue Reading Set a %coverage threshold during a hmmsearch using HMMer

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…

Continue Reading How to merge HMM files for HMMSearch?

tmhmm installation and running

tmhmm installation and running 0 Hi, I am trying to predict transmembrane protein using tmhmm-2.0c. I have changed the path of perl like as following. which perl /usr/bin/perl perl -v This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi (with 44 registered patches, see perl -V for…

Continue Reading tmhmm installation and running

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…

Continue Reading RNAmmer running

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…

Continue Reading IMPUTE2 – problem with MCMC

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…

Continue Reading blast protein alignment

Unable to locate package cuda-command-line-tools – TensorRT

Description Hi! I would like to get some help while building the docker file in AlphaFold2. when I execute the command following sudo docker build -f docker/Dockerfile -t alphafold . I got the following error. Get:22 archive.ubuntu.com/ubuntu focal-backports/main amd64 Packages [2668 B] Fetched 19.7 MB in 6s (3575 kB/s) Reading…

Continue Reading Unable to locate package cuda-command-line-tools – TensorRT

biopython write fasta

Step 1 − Create a file named blast_example.fasta in the Biopython directory and give the below sequence information as input. 3. “””Bio.SeqIO support for the “fasta” (aka FastA or Pearson) file format. Then we save this line of text to the output file: Now we have finished all the genes,…

Continue Reading biopython write fasta

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…

Continue Reading Dice Bioinformatics Engineer Vacancy 2021

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…

Continue Reading bad file format in HMM file

Flow Cytometry and DNA Sequenzing Facility

BD Influx Sorter, a globally unique prototype equipped with fiber optics and octagon/trigon arrays. BD Influx Sorter, a globally unique prototype equipped with fiber optics and octagon/trigon arrays. Flow Cytometry Fluorescence-Activated Cell Sorting (FACS) is a technology that enables qualitative and quantitative analysis of cell mixtures and sorting by individual…

Continue Reading Flow Cytometry and DNA Sequenzing Facility

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…

Continue Reading BLAST versus HMM search

gmod how to animate ragdolls

Now that you know nearly all the possibilities in this mod, let’s go even more deeper. Oct 15, 2019. Continue browsing in r/gmod. The original TF2 on the other hand is very easy to face pose, because you can literally move just 1 silder, and then you got a “happy…

Continue Reading gmod how to animate ragdolls

South Africa Job Availability : bioinformatics

Search within r/bioinformatics r/bioinformatics Read more here: Source link

Continue Reading South Africa Job Availability : bioinformatics

Biopython Contact Map | Contact Information Finder

Listing Results Biopython Contact Map Protein Contact Maps using Biopython Warwick 9 hours ago Warwick.ac.uk View All Protein Contact Maps using Biopython. When working with protein 3D structures, a contact map is usually defined as a binary matrix with the rows and columns representing the residues of two different chains….

Continue Reading Biopython Contact Map | Contact Information Finder

From FASTA to 3D protein? : bioinformatics

Search within r/bioinformatics r/bioinformatics Read more here: Source link

Continue Reading From FASTA to 3D protein? : bioinformatics

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…

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

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…

Continue Reading alphafold colab github

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…

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

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:…

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

Difference between job titles? : bioinformatics

Search within r/bioinformatics r/bioinformatics Read more here: Source link

Continue Reading Difference between job titles? : bioinformatics

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…

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

[Hands-on for beginners] Read kaggle’s “Predicting Home Prices” line by line (Part 2: Checking Missing Values)

Click here for the first content This is the second part of a project to make a note of the contents of hands-on, in which everyone will challenge the famous “House Price” problem of kaggle. It’s more of a memo than a commentary, but I hope it helps someone somewhere….

Continue Reading [Hands-on for beginners] Read kaggle’s “Predicting Home Prices” line by line (Part 2: Checking Missing Values)

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,…

Continue Reading How are the HMM cutoff scores in TIGRFAMs determined?

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…

Continue Reading Can HMMs detect partial proteins sequences?

Easy Way To Get 3′ Utr Lengths Of A List Of Genes

Easy Way To Get 3′ Utr Lengths Of A List Of Genes 4 Hi, as the title says really, I’m wondering if there is any tool available that would allow me to drop in a list of say entrez gene ids and get their corresponding 3′ UTR lenghts? Thanks for…

Continue Reading Easy Way To Get 3′ Utr Lengths Of A List Of Genes

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…

Continue Reading get only one representative fasta sequence per family

VEP plugin uses

VEP plugin uses 0 It is a small question, I downloaded all plugins and wrote in the input script to get plugin experimental functionalities (I am using merged cache Ref_Seq & Ensembl both). # make a file with a single variant using bash echo “17 43071077 43071077 T/C + variant_1″…

Continue Reading VEP plugin uses

DNA methylation EPIC array and ChromHMM

DNA methylation EPIC array and ChromHMM 0 Hello, I have DNA methylation data obtained by the EPIC array and I would like to use this data to check for chromatin states using the ChroHMM software. I understand that the data must be in a binary format, grouped by each 200bp,…

Continue Reading DNA methylation EPIC array and ChromHMM

Interpreting dbNSFP prediction scores

Interpreting dbNSFP prediction scores 1 How should I interpret for example, SIFT score: SIFT_pred = T;T;T;T;D;T SIFT_score = 0.138;0.138;0.138;0.138;0.042;0.157 From dbNSFP documentation, I understand the meaning of D and T D: Deleterious (sift<=0.05); T: tolerated (sift>0.05) My question is: Why there are multiple values of both pred and score in…

Continue Reading Interpreting dbNSFP prediction scores

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…

Continue Reading MAKER genome annotation error with SNAP ab initio prediction

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…

Continue Reading Comment: alphafold online availability and use case

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…

Continue Reading alphafold online availability and use case

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…

Continue Reading So many variants detected.

Inquiry related to vcf file and formatting

Hello everyone, I am trying to run predixcan software. But its showing error as segmentation fault implying that there is something wrong with my vcf files. I am sharing the header of vcf file. ##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description=”MLE Allele Frequency Accounting for LD”> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description=”Average posterior probability from MaCH/Thunder”> ##INFO=<ID=RSQ,Number=1,Type=Float,Description=”Genotype imputation quality from…

Continue Reading Inquiry related to vcf file and formatting

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….

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