Biostar

11,968 results • Page 2 of 240

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 26 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 26 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 27 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 27 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 27 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 28 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 28 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 28 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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 4 weeks 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...68.8 167.5 100.7 362.5 101.4 ... $ Protein H : num 2.11 8.6 882.38 92.81 4.59 ... $ Protein I : num 0 8.39 13.65 14.51 0 ... $ Protein J : num 1714.73 3654.55 537.31…

microarray combat batch-effect median-normalization

updated 4 weeks 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 4 weeks 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 4 weeks ago • Corentin

The situation is as follows Collaborators used a protein array to detect changes in protein abundance between two experimental groups. The simplified original design was...The situation is as follows Collaborators used a protein array to detect changes in protein abundance between two experimental groups. The simplified original design was something like this: sample /// expGroup /// su…

statistics protein-array batch-effect

updated 4 weeks ago • s.lima.diogenes

I am trying Circos plotting for the first time, to plot pathway nodes for proteins. I followed a posting on Medium to see how to set it up and run it. I have a short list of 8 proteins that I wanted to plot...pentraxin 3', 'serpin E1', 'cyr61', 'coagulation factor 3', 'cxcl16', 'mcp-1', 'igfbp3', 'ip10'] proteins = '%0d'.join(protein_list) url = 'https://string-db.org/api/tsv/network?iden…

CircosPlot

updated 4 weeks ago • hniels01

eg structural diversity. Is there a way to achieving the above? I have downloaded and installed a local copy of the RepeatMasker program, and run the tool locally on my sequence, however this appears to focus more on the annotation

sequence RepeatMasker pacbio

updated 4 weeks ago • epaminonda

the Gene_id from mRNA-seq to Uniprot Gene_name? What are the best common identifiers for mRNA and protein data

rna-seq tmt nomenclature proteomics

updated 4 weeks ago • ntsopoul

SVTYPE=INS;END=41473873 GT:DP 1:150 Ensembl's VEP correctly classifies the <dup> variant as protein coding SnpEff incorrectly classifies is an intron variant For now, I am just converting the short <dup> entries into

snpeff

updated 4 weeks ago • kirill.zaslavsky

will be enabled to build their own scalable, reproducible bioinformatic pipelines which can be run locally, on high-performance computing clusters or even in the cloud. The course layout has been adapted to the needs of beginners

workshop RNA-seq nextflow DNA-seq

updated 4 weeks ago • David Langenberger

and report wide variation in RE dynamics across groups. Analysis of associations between REs and protein-coding genes revealed dynamic evolution at the interface between REs and coding regions across insects, including

herald

updated 4 weeks ago • Biostar

what are the good Python models/packages to predict small molecule (SMILES input format) binding to proteins ? Any further information - papers, yours experience, whatever - is welcome ! PS I am aware of: Chembert - (created some notebook...https://www.kaggle.com/competitions/leash-BELKA/code To predict small molecule binding to three proteins Dataset includes 90 millions small…

SMILES

updated 4 weeks ago • Alexander

file available In NCBI. I used RNAseq data available for the same organism In EBISRA and a set of proteins available in NCBI as input to BRAKER3 as evidence. I got the BRAKER 3 result as a GFF3 file. it gave the mRNA positions...in the genome but did not give the name or id of proteins or mRNA. how should I annotate further

annotation BRAKER3 genome

updated 5 weeks ago • manaswiniparija3

I generated a high quality de novo genome assembly which has been annotated using previously published isoseq data from the species. This genome is now the Refseq for the species. I am currently writing a manuscript detailing the assembly. My PI suggested that I add a quick biologically relevent analysis to the text to show the utility of my genome. Specifically, she said I should investigate if …

blast duplication paralog genome

updated 5 weeks ago • brimaloney24

I need a small protein that has multiple chains, but the total number of atoms will not be more than fifty. I need this to experiment with in...my software. Can you suggest such a protein PDB

protein pdb protein-databank

updated 5 weeks ago • 4fzcgueyp5

everyone, I'm looking for an alternative tool to DynaMut that performs analysis and prediction of protein stability changes upon mutation. Or if there's any alternative way to conduct this analysis. Thank you very much to

mutation analysis

updated 5 weeks ago • marco.barr

Hi All, Exploring the relationship between mRNA and protein expression levels is crucial for several reasons. It helps in understanding the fundamental aspects of gene expression...regulation, including post-transcriptional modifications, protein stability, and translation efficiency. Additionally, analyzing mRNA-protein correlations can provide insights

correlation protein mRNA

updated 5 weeks ago • Shicheng Guo

as a method, facilitates gene silencing through the targeted degradation of mRNA, thus reducing protein synthesis without directly altering the DNA. On the other hand, CRISPR-Cas9 technology offers a more direct approach

DepMap

updated 5 weeks ago • Shicheng Guo

counts=sample1_GEX) sample1_ADT<-Read10X(data.dir = "") sample1_GEX_seurat[['Protein']] = CreateAssayObject(counts = sample1_ADT$`Antibody Capture`) I am a beginner on this field, so I am afraid this is a very

Seurat scRNA-seq ADT Cite-seq GEX

updated 5 weeks ago • gdfsnkfns

Dear all, When i use EVidenceModeler to do the genome annotation,it get the error: ---------- successfully changed directories to acu.partitions/GWHBGBO00000001/GWHBGBO00000001_10890001-10990000 -reading genomic sequence. ** Processing features (+) -finding all potential splice sites, looking for GT/GC donors and AG acceptors. -finding all potential star…

EVidenceModeler annotation genome

updated 5 weeks ago • peanut

Hi Community, I have 17 metagenomically assembled genomes (MAGs). I want to annotate the protein of these genome using Pfam. I want a step by step guideline for the annotations in Linux bash. My idea is: I need to download

annotation metagenomic Protein Pfam

updated 5 weeks ago • Md Moinuddin

for processing short read data. This will include learning about different approaches for annotating protein-coding genes in eukaryotic species via projection and evidence guided gene prediction. Discuss the challenges

Genome-Assembly RNA-seq Genome-Annotation

updated 5 weeks ago • carlopecoraro2

Hello all, I am new to R programming and I would like your help in suggesting a strategy to solve the following question. I have gene expression data and protein expression data which has the same samples. I want to identify differentially expressed genes by comparing both datasets. So for this I have tried first merging both the datasets and performing differential expression using limma, then …

gene-expression R protein-expression Differential-gene-expression Volcano-plot

updated 5 weeks ago • vin23

I carried out differential expression analyses only on protein-coding genes because that is what I was interested in. Now after a while, I am considering looking into lncRNAs as well...Should I run DGE on just the lncRNAs or combine protein-coding and lncRNAs and rerun it together? The number of genes analysed changes a lot in both these situations. This

differential-gene-expression RNA-seq

updated 5 weeks ago • firestar

Hi Community, I have the next doubt, if I'm only interested in protein coding genes it's a good practice to obtain the ORFs from my transcriptome (de novo assembled) using for example Transdecoder

differential-gene-expression RNA-Seq ORFs

updated 5 weeks ago • pablo61991

slurm_extra="--gres=gpu:1" restart-times: 1 max-jobs-per-second: 10 max-status-checks-per-second: 1 local-cores: 1 latency-wait: 60 jobs: 100 keep-going: True rerun-incomplete: True printshellcmds: True scheduler: greedy use-conda

Parabricks gpu snakemake slurm

updated 5 weeks ago • raphael.B

amp;& autoconf && ./configure --enable-libgsl --enable-perl-filters --with-htslib=/usr/local/lib/pkgconfig/ make > /home/jaime/dev/cgat-flow/conda-install/envs/cgat/bin/x86_64-conda-linux-gnu-cc > -Wall -march=ntorize...strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/ja/envs/cgat/include -I. -I/usr/local/lib/pkgconfig//includ…

error BCFTools vcfmerge.o install

updated 5 weeks ago • jaime alvarez

from all RNA samples using Ribo-Zero (epicentre) prior to generating libraries. In principle, my protein does not bind rRNA although I cannot rule it out. Taking into account that the isolated RNA is immunoprecipitated

rRNA RIP-seq

updated 5 weeks ago • CrisRisu

Could someone assist me in identifying non-paralogous protein or nucleic acid sequences without relying on CD-HIT tools? Since this web server is no longer operational, what steps

CD-HIT

updated 6 weeks ago • koushiksarker1977

field of bioinformatics, our endeavor requires maintaining massive quantities of genetic sequences, protein structures, and other biological data. Using Mongoose as the MongoDB object modeling tool, we want to effortlessly...the complex relationships inherent in bioinformatics datasets. How can we model genetic sequences, protein structures, and other biological entities effectively using Mongoos…

mongodb mongoose

updated 6 weeks ago • zainabi8077

Function to align reads to references and extract reads for each gene seperately classify_reads() { local input_fastq="$1" local output_prefix="$2" ### align reads to reference sequences minimap2 -ax map-ont "$gene1_ref" "$input_fastq

classification reads nanopore

updated 6 weeks ago • maevalefeuvre

Hello all, I am building a pipeline to perform searches on the latest ensembl bacteria release locally. However, in trying to parse the data to get more information from other databases I've come across an issue. Since release...from the ensembl release, these contain a crossref to the Genbank id for the whole contig that gene/protein is one (e.g. LMIU01000024.1). Then I need to access that…

database parsing cross-reference ensembl

updated 6 weeks ago • J

Gene.Ontology.IDs LOC130612038 130612038 cysteine and glycine-rich protein 1-like GO:0005634; GO:0005737; GO:0008307; GO:0030018; GO:0042805; GO:0045214; GO:0060537 LOC130612042 130612042 leucine...rich repeat-containing protein 74B-like GO:0005509; GO:0005515 LOC130612045 130612045 uncharacterized protein LOC1306120…

ClueGo Cytoscape

updated 6 weeks ago • Nicolas

some chemical/substrate information in there too. Not just sequence determines whether or not a protein is an ortholog. Is there a database that has this? neither yeastgenome.org nor Alliance have any info. Searching produces

database orthologs

updated 6 weeks ago • dec986

current time: 04/04/2024 23:37:47 ***** 2024-04-04 23:37:47 INFO: Configuring BUSCO with local environment 2024-04-04 23:37:47 INFO: Running genome mode 2024-04-04 23:37:47 INFO: Downloading information on latest versions...current time: 04/04/2024 23:37:47 ***** 2024-04-04 23:37:47 INFO: Configuring BUSCO with local environment 2024-04-04 23:37:47…

duplicate BUSCO.

updated 6 weeks ago • Sony

Hello, I'm sorry if this is poorly written, it's my first time writing code with Snakemake, and my professor has given no instructions on how to deal with troubleshooting! I haven't found much help online because we're writing in Python, not Bash. I am getting an error code `Expecting rule keyword, comment or docstrings inside a rule definition` with the line `genotypes= pd.read_table(str(input))…

python snakemake

updated 6 weeks ago • 888pea

Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: Europe/Berlin tzcode source: internal attached

RobustRankAggreg microarray R rankMatrix

updated 6 weeks ago • hagl

and lacking in maintenance. As an important resource for understanding the relationship between protein variations and associated diseases, I am seeking recommendations for the most up-to-date and well-maintained database

Uniprotkb

updated 6 weeks ago • Shicheng Guo

11,968 results • Page 2 of 240

Recent Votes

Answer: Q: GenomeScope input and how to interpret the results

Answer: How to find tandem duplications pattern in a DNA sequence

A: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Seque

C: Snakemake vs. Nextflow: strengths and weaknesses

Answer: workflow management system : WDL, CWL, Ruffus, SnakeMake, etc

Sequence alignment on split read event such as inversion, duplication and complex nested events.

ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award

Recent Locations • All