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11,952 results • Page 1 of 240

Hello, how do I import a fastq file from my local windows computer into fluent terminal wls

Fastq

updated 7 hours ago • oumo

has proven more stubborn. Output for 'which conda' yields the following: conda () { \local cmd="${1-__missing__}" case "$cmd" in (activate | deactivate) __conda_activate "$@" ;; (install | update | upgrade | remove | uninstall) __conda_exe

biopython conda mamba pycosat

updated 7 hours ago • kacollier

and recognising that ATG is a start codon and placing the original contig first via assumption for protein synthesis via transcription Translate the DNA sequence into a protein sequence DNA Sequence: ATG-CGC-TGC-ATG-ATG...GGG-G Reading frame: ATG CGC TGC ATG ATG GAT ACC CCG GTC GCT TCG CGG CCG CTA ATC GGG G Translated Protein Sequence: Met-Arg-Cys-Met-Met-Asp-Thr-Pro-Val-Ala-Ser-Arg-Pro-Leu-Il…

genetics contig assembly dna bioinformatics

updated 12 hours ago • rackbersingh

extracted from KEGG-KASS or by exploring alternative methods to utilize bacterial genome assembly or protein sequences for pathway identification. Please suggest an alternative tool or method

KEGG-KASS WGS Pathway denovo

updated 17 hours ago • mathavanbioinfo

attached to the pore. Immobilization: In the case of protein-based nanopores, they are immobilized on a resistive membrane. Kinetic Proteins: Special motor proteins are employed...of DNA or RNA. Key components involved in nanopore sequencing include: Reader: Transmembrane proteins (such as protein nanopores) are used as readers to detect the nucleic acid passing through the nanopore. These …

biotech

updated 1 day ago • usa.cd.genomics

characterization. Western Blotting [Western blotting][1] helps identify specific exosomal proteins by targeting markers such as CD63, CD9, and Alix. Creative Proteomics employs Western blotting to validate exosome...Mass spectrometry-based [proteomic analysis][2] enables the comprehensive identification of exosomal proteins, shedding light on their functional diversity. Creative Proteomics' e…

biotech

updated 1 day ago • dorawestgogo

pain despite injuries. This discovery not only elucidates the physiological role of membrane proteins but also underscores their potential as therapeutic targets. Through advanced proteomic techniques, Creative...are paramount in cardiovascular health. The Sodium-Potassium Pump (Na+/K+ ATPase), a transmembrane protein, maintains cellular ionic balance critical for heart function. Alterations in N…

biotech

updated 1 day ago • dorawestgogo

via CellPhoneDB (CPDB) package and I am wondering how can I limit the results to cell surface proteins? This is the dats's head: > colnames(cpdb) [1] "id_cp_interaction" "interacting_pair" "partner_a" "partner_b" "gene_a" [6] "gene_b

cellphonedb cpdb cell_surface_proteins

updated 2 days ago • piotto

I analyzed a protein-protein interaction analysis via CellPhoneDB package v5. The out put are these files: 1- Deconvoluted 2- Significant_means

cpdb visulization cellphonedb

updated 2 days ago • piotto

following error: ```r install.packages("gmwm") Installing package into ‘C:/Users/najafi/AppData/Local/R/win-library/4.2’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘gmwm’ is not available for this version

updated 3 days ago • snajafy

following error: ```r install.packages("imudata") Installing package into ‘C:/Users/najafi/AppData/Local/R/win-library/4.2’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘imudata’ is not available for this version

updated 3 days ago • snajafy

Hello, I am trying to return interaction partners for proteins using the STRING-DB API in python, but for many of the proteins it seems unable to find them, even though when I search...response object, it says this: Error ErrorMessage not found Sorry, STRING did not find a protein called 'RPS4Y1' in the taxon '9606'. Generally, STRING understands a number of different names/symbols fo…

STRING-DB protein STRING-DB-API

updated 3 days ago • brandon

Published a small extension of MutaFrame, to: - Show conserved regions and SNPs of the Sars-Cov-2 receptor ACE - 2 - Show conserved regions of the Sars-Cov-2 spike protein based on comparison of Sars-Cov-1/HIV - Different isoforms of ACE 2 - Alignment of 166 Sars-Cov-2 genomes, and mutation hot...and SNPs of the Sars-Cov-2 receptor ACE - 2 - Show conserved regions of the Sars-Cov-2 spike prote…

sequence alignment SNP genome

updated 4 days ago • Ibrahim Tanyalcin

Hello All, I have a quick question that I need some advise about. I am running differential expression on a set of proteins and I am using Limma package in R. I have three replicates of positive control, three rep. of treatments and 3 rep. of controls. I would like to compare the expression level differences of the treatment vs the control data. Though the expression level of the significant…

RNA-seq Differential-expression

updated 5 days ago • SHN

the SNV and indel variants for each patient, filtering them to retain only the variants affecting protein-coding genes (I have retained the unfiltered ones as well). Currently, I'm facing a problem. To obtain the necessary features

formats vcf fastaq HLA_imputation HLA_typing

updated 5 days ago • Javier

The data contains multiple barcodes.tsv.gz,features.tsv.gz and matrix.mtx.gz files of both RNA and protein. How to analyze these datasets?. Thank you in advance. I know the basic sc-RNA analysis using Seurat, but how to do processing

multimodal-analysis single-cell

updated 6 days ago • nithya

I give Up!!!! I am unable to install a local version of provean! I tried the v4 nr database, latest release of provean, but always stuck at that dreaded `Segmentation...I give Up!!!! I am unable to install a local version of provean! I tried the v4 nr database, latest release of provean, but always stuck at that dreaded `Segmentation Fault, core dumped` error. Does anybody have a working versi…

variant Provean

updated 6 days ago • Arun Sai Kumar

structure using R. Additionally, you'll receive training in two statistical approaches for studying local adaptation: Sambada and LFMM. The course will also address the crucial task of interpreting and validating results

LFMM Landscape-Genomics Sambada R Local-Adaptation

updated 7 days ago • carlopecoraro2

to generate a pse-pssm file to run a programme, ASPIRER, for identifying unconventionally secerted proteins. However I am running into issues with it the code I used to generate the pssm file is as follows: ``` psiblast \ -db nr \ -query

fasta pse-pssm pssm POSSUM

updated 8 days ago • rianna.collins

I have a large fasta file of new species, I want to find extract a particular protein sequence. I also know a protein sequence of a similar species, which potentially can be used for finding the protein

fasta alignment blast

updated 8 days ago • anna

Hi all, I've been working on analyzing my single-nuclei RNAseq data using the general Seurat pipeline followed by DoubletFinder. I'm using the following [walkthrough as a guide][1] for my doublet identification and removal. When running my code (see below) I get an error: Error in `[[<-`(`*tmp*`, i, value = temp2.singlets) : [[<- defined for objects of type "S4" only for su…

Seurat single-cell DoubletFinder single-nuclei SeuratObject

updated 8 days ago • sarphilsar

Hello, I have a database of hydrolases (in particular, plastic degrading enzymes) and i would like to rerieve the positions of the residues in the catalytic triad (that are the active site residues annotated on UnipPot) for each enzyme. Is there a way I could retrieve those residues and respective positions in the sequence, programatically? I have seen other similar posts but a lot of the …

Uniprot PDB Proteins

updated 10 days ago • Mariana

I'm trying to update to the latest version of R on Ubuntu with the following command: ``` $sudo apt-get -y install r-base ... Reading package lists... Done Building dependency tree Reading state information... Done r-base is already the newest version (4.4.0-1.2004.0). The following packages were automatically installed and are no longer required: ... ``` I've done this many times …

installation update R apt-get

updated 10 days ago • Bosberg

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](/herald/). This edition of the Herald was brought to you by contribution from [Istvan Albert](https://www.biostars.org/u/2/), and was edited by [Istvan Albert](https://www.biostars.org/u/2/)…

herald

updated 10 days ago • Biostar

from [rcsb][1] for my research paper. I have seen many pdbs have less residues in a chain of a protein than the full FASTA sequence. Most likely, the cause is that they were unmodeled due to its going missing during the

PDB FASTA

updated 10 days ago • Nafi

as all the enzymes within 1.1.1 level?** * **If there is a pathway that requires 1.1.1.2 would a protein annotated as 1.1.1.- be sufficient

ontology metagenomics database enzymes genomics

updated 12 days ago • O.rka

I try to BLAST a list of queries (queries.fasta) against a local mirrors of NCBI nucleotides database (`nt`) and taxonomic database (`taxdb`). I run the following script (in R environment...I try to BLAST a list of queries (queries.fasta) against a local mirrors of NCBI nucleotides database (`nt`) and taxonomic database (`taxdb`). I run the following script (in R environment): system2

blast ncbi taxid taxonomy

updated 14 days ago • Begonia_pavonina

MaxQuant output quantifies the protein intensity in two ways : Intensity (called LFQ intensity in a label-free experiment) : The combined intensity of the peptides...MaxQuant output quantifies the protein intensity in two ways : Intensity (called LFQ intensity in a label-free experiment) : The combined intensity of the peptides of the protein. iBAQ : A score attempting to make the intensity …

protein maxquant

updated 14 days ago • Aspire

I need an example of a small globular protein that has disordered alpha-carbons in its chain. Can you propose one? Can you give me an example of a protein (PDB) that has

protein pdb alpha-carbon

updated 14 days ago • 4fzcgueyp5

Hello! I have a multiFASTA file that contains a set of aminoacidic sequences that I want to compare in terms of sequence identity, what tool do you recommend me for this? I want all vs all comparisons so I can build a heat map.

protein FASTA alignment

updated 14 days ago • v.berriosfarias

I was thinking of pursuing a Machine Learning project to familiarize myself more with the topic. I want to create a model to predict the source of an outbreak based on sequence features from DNA sequences isolated from various countries. Let's assume there's a virus X, and virus X has a conserved protein encoding region of about 1000bp long. This region is used to predict the genotype of the …

DNA ML

updated 14 days ago • biochugs

Name=grxB;gbkey=Gene;gene=grxB;gene_biotype=protein_coding;locus_tag=pgaptmp_000003 GCA_007218495.1 Protein Homology CDS 1959 2606 . - 0 ID=cds-pgaptmp_000003;Parent=gene-pgaptmp_000003;Name=extdb:pgaptmp_000003;Ontology_term...gbkey=CDS;gene=grxB;go_function=glutathione-disulfide reductase (NADPH) activity|0004362||IEA,protein binding|0005515||IEA;go_process=glutathione metabolic process|000674…

pangenome PGAP NCBI roary Prokka

updated 15 days ago • pramach1

https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/RoseTTAFold.ipynb) for protein model prediction. However, I came across this error which I was trying to solve for couple days. ![enter image description

modeling Google Colaboratory RoseTTAFold protein

updated 15 days ago • benguyarenbeyaz98

result in fewer biased sites. We find that end-to-end alignment reduces bias at indels relative to local aligners. submitted by: [Istvan Albert](https://www.biostars.org/u/2/) --- ### [ScienceDirect](https://www.sciencedirect.com/science

herald

updated 15 days ago • Biostar

wondering which software tool bioinformaticians generally use for secondary structure assignment of protein chains. I know two tools DSSP and STRIDE. However, their accuracies are around 53% and 70%, respectively. So, are DSSP and

secondary-structure protein

updated 15 days ago • 4fzcgueyp5

search for in a file or a annotation program**: Like this from NCBI for TNNT1: This gene encodes a protein that is a subunit of troponin, which is a regulatory complex located on the thin filament of the sarcomere. This complex...calcium, troponin T, which binds tropomyosin, and troponin I, which is an inhibitory subunit. This protein is the slow skeletal troponin T subunit. Mutations in this ge…

annotation visualisation NCBI Uniprot RNA

updated 15 days ago • Amélie

each pair of sequences. For the moment, I am performing a multiple sequence alignment at the protein level using MUSCLE v5 followed by trimming and back-translating the protein alignment into a coding sequence alignment

Pairwise-Alignment Genomics Ka-Ks

updated 16 days ago • maxime.policarpo

Hi, I am trying to hunt some toxin genes in my genomes. I used antismash to look for the secondary metabolites region and tried annotating my contig with reference sequence. blasting the two sequences, I get no similarity in nucleotide sequences but somewhat similarity when blasting protien sequences. Is this possible? I am new to metagenomics, any advice related to this problem will be great.

gene-hunting blast

updated 16 days ago • Abeer

Hello! I have a database of proteins, where I have various information for each protein, including its UniProt ids, protein sequence, and more. I'll be working...Hello! I have a database of proteins, where I have various information for each protein, including its UniProt ids, protein sequence, and more. I'll be working on metagenomics and running my sequences against the sequences of some …

Nucleotide Genomic Sequence Uniprot Proteins

updated 17 days ago • Mariana

of the relative enrichment or height of called peaks. I think ChIP-seq is a method to detect protein enrichment sites in genome. My question is, why these enriched peaks have different height when we check it in bigwig...track. In my view, peak height means the research get more protein bound fragments from cell population, and there are higher fraction of cell that have protein bind to a peak …

ChIP-seq

updated 17 days ago • HyperEvo

please someone explain how we find protein sequence (uniprot kb) which does not have any structure or predicted structure for predicting structure in swiss

homology-modeling swiss-model

updated 17 days ago • Ayush

I want to make protein structure for that protein DNAH17. For this purpose , I take protein sequence from UniProt:https://www.uniprot.org...I tried AlphaFold2.ipynb from google colab but it was not executed due to the big size of protein. Should I try modeller

BLAST Protein-Structure-Prediction

updated 17 days ago • anasjamshed

instead of any kind of species/strain identifier. I know that I should be able to collect protein sequences from the blastp results into a file, but I do not know how to do this. I would then need to blastp these sequences...against the non-redundant protein database and write a file that contains information about the taxonomy of the the top blastp hit. I don't need the amino...of bacteria…

shotgun metagenomics blastp taxonomy

updated 19 days ago • rebecca.calvo

R][1] Remember: All versions of R are always installed in /opt/R, while a symlink is placed in /usr/local/bin/R. So the command "which R" always returns the symlink, not the installation location or version First Installation...bin/R --version # step 7 - verify installation sudo ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R # step 8 - create R symlink (first installation only) sudo l…

R Ubuntu Linux Bioconductor Rstudio

updated 19 days ago • BioinfGuru

Hi, I'm using Avogadro 1.2.0 to edit a FAD metabolite and add to its structure a couple of nucleotides so that it resembles a ligand for IFIT proteins. As of my knowledge, there aren't reports of a chemical structure validated with such characteristics, how could I...metabolite and add to its structure a couple of nucleotides so that it resembles a ligand for IFIT proteins. As of my knowledge…

structure cap validation metabolite

updated 19 days ago • Rodolfo Adrián

on molecular docking and I want to download some pdb's as pdb format according to search (name of protein, name of organism) on rcsb.org. Can someone help me if there is a way to do it, how it can be done? Thanks for any help

rcsb pdb

updated 20 days ago • iamsmor

import Read from AutoDockTools.MoleculeTools import Mol from AutoDockTools.MoleculeTools import Protein from AutoDockTools.MoleculePreparation import AD4ReceptorPreparation ``` and I get error again ```py from AutoDockTools.MoleculeTools

python python3 autodock

updated 20 days ago • iamsmor

Protein D : num 24.5 26.4 109.5 90.6 75.3 ... $ Protein E : num 71.9 73.3 186.9 93.1 100.6 ... $ Protein F : num 148 208 192 623 184 ... $ Protein G : num...Protein K : num 148 100 206 743 17 ... $ Protein L : num 824 601 2597 968 582 ... $ Protein M : num 650 296 999 358 478 ... $ Protein N : num 616 294 1120 …

microarray combat batch-effect median-normalization

updated 20 days ago • Dominique

samples had a grand total of 100-150 called peaks. My first hunch is that I might be dealing with a protein that has very few binding sites on the genome and that partially explains the low QC scores. If anyone has worked with...it before, the name of the protein being immunoprecipitated is Rev-erb-alpha. I found similar ChIP-seq experiments that reported high variability

ChIP-Seq batch-effect sequencing

updated 21 days ago • dmj6ab

and I just wondered if there was a better way to do this. For example is it worth it to download a local version of the mart

biomaRt getBM R

updated 22 days ago • Corentin

11,952 results • Page 1 of 240

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