Biostar

11,930 results • Page 1 of 239

Can anyone recommend some methods/tools for predicting the subcellular localization of proteins. e.g. which of a group of genes is likely to be extracellular. Wikipedia has a nice article...on the topic: protein subcellular localization It even lists some tools. These predictors tend to be specialized for proteins in different...a review of informatic methods related to the problem. Recommended…

protein annotation prediction

updated 12.4 years ago • Malachi Griffith

implemented this strategy outlined in this paper? Specifically for bacteria? It describes how to localize protein products subcellularly. I am wondering if there is a one-button solution for subcellular localization...for bacteria. http://www.nature.com/nprot/journal/v2/n4/abs/nprot.2007.131.html Locating proteins in the cell using TargetP, SignalP and related tools Olof Emanuelsson1, Søren…

updated 10.8 years ago • Lee Katz

Hi, I'm analyzing the subcellular localization of the proteins of a constructed pangenoma, using Cello 2.5 and PSORTB.I wanted to ask for some...refine the output of each program and reach a consensus since I'm analyzing a pangenome with 4800 proteins with PSORTB and I get 1900 proteins whose subcellular localization is undefined. Is there any other program to analyze

localization psortb prediction cello subcellular

updated 2.7 years ago • BATMAN

Hi, guys. I want to know the specific content of proteins in different subcellular localization. Does anybody know where I can find this kind of data? And I wonder if there...is some high-throughout way to measure the protein content

protein subcellular localization

updated 6.3 years ago • xidianbill

Hi everyone, Protein localization (subcellular localization) is an active field of research. In previously published papers on this problem...people exclude the homologous proteins from data sets. I was wondering if any body knows the reason of excluding homologous proteins?! Is it for preventing

subcellular prediction homology protein

updated 7.0 years ago • ruhi.jamali

Hi all, I try to annotate subcellular localization for all human, rat, mouse proteins. My goal is to add clear and simple information to manage (use a very...already performed a good annotation focused on secreted, using several db and papers. For the other localization, I'm going to look at eSLDB, LOCATE, comPPI.. Other possibility will be to used a predictor but ideally, I want to make...and u…

protein localization

updated 7.0 years ago • bzhtgb

Please can anyone help me with a method to predict the subcellular localization of proteins in whole proteome of an organism? Is there a web server that accepts a whole proteome

Protein Proteome Localisation Prediction

updated 2.9 years ago • Ammar Danazumi

BLAST2GO, PFAM and Interproscan. However, I wonder if there is any tool that can be used to annotate proteins without any names directly (not just focus on function or subcellular localization like GO) such as HAMAP (enter link

updated 10.0 years ago • Cacau

I'm trying to find the subcellular localizations of a list of genes using biomaRt but I keep getting the error: `Query ERROR: caught BioMart::Exception

R biomaRt

updated 3.8 years ago • andyincolorado

Dear All, I'm writing to inquire if anyone has an R or Python script that can extract subcellular locations (compartments) from the GeneCards database. Ideally, the script should take a gene name as input and...return a data frame or equivalent structure that displays the subcellular compartments and their corresponding confidence scores, just like the information presented on the GeneCards...…

Genecards

updated 23 days ago • Shicheng Guo

I want to find list of proteins of fungus from uniprot which Subcellular location have Manually-assigned evidence and not electronically assigned

uniprot query

updated 9.1 years ago • Kaiser Ahmed

to get a list of genes and the place in the cell where they are being translated and a list of genes(/proteins) and the place in the cell they are usually in after being translated(localization data) I can't find anything like

localization genes

updated 2.8 years ago • datacollector

Hello, I have around 400 protein sequences which have no sequence similarity, no identifiable protein domains and no identifiable motifs. What steps...should I take in order to characterize these proteins, both in function and strucure? My initial thoughts were as follows: 1) Compute physiochemical properties such as...aliphatix index, and grand average of hydropathicity. 2) Predict secondary s…

protein sequence modeling

updated 9.4 years ago • James Ashmore

I have done a LC-MS/MS analysis of the proteins of a gram-positive bacterium. I need to differentiate the membrane proteins from the others, but i only have the accession...number. Do you know how I can know the subcellular location of each of the thousand proteins that I have

genome

updated 4.8 years ago • Estbioq

know of a tool that accepts as an input a list of different genes and categorize them according to subcellular localization (e.g. which of the genes code to proteins that are found on the cellular surface, which are transcription

RNA-Seq proteins subcellular genes

updated 5.4 years ago • akivab2

there any standalone tool which do all primary analysis, secondary structure analysis for a bulk of protein sequence.? (e.g. like protpram -molecular weight, theoretical pI, amino acid composition, atomic composition, extinction...estimated half-life, instability index, aliphatic index and grand average of hydropathicity), subcellular localization, signalP & Transmembrane helix prediction…

protein protein-structure

updated 9.0 years ago • jackuser1979

Q: Is there a metabolite localization database for a model organism? How: literature mining, MALDI imaging, Raman-spectroscopy based methods such

database

updated 10.7 years ago • Lo Sauer

Hi, I am seeking any evidence (paper or other reference) for co-localization of two proteins lead to interaction in PPI network. Any help will be greatly appreciated. Thanks

PPI co-localization

updated 24 months ago • mahdijalili

www.ncbi.nlm.nih.gov/pmc/articles/PMC9220970/) as an example. The paper repeatedly talks about **local**, **non-local**, and **external** features. Some of them are distance, geometry, angle, hydrogen bond count, etc. What do "*local*", "*non-local...and "external" features mean regarding protein secondary structures

protein assignment secondary-structure

updated 12 months ago • 4fzcgueyp5

What is the easiest way to transform local coordinates on a protein/transcript to genomic coordinates (given accession number

python ucsc cruzdb

updated 5.7 years ago • tim.ivanov.92

amp;cellId=59][2] PS (From ChatGPT ) **Question:** what are the recommended parameters for the local protein alignment ? ChatGPT The choice of parameters for local protein alignment depends on the specific algorithm...or tool being used. However, I can provide you with some commonly recommended parameters for local protein alignment using the popular tool BLAST (Basic Local Alignment Searc…

protein alignment

updated 10 months ago • Alexander

Secondary structure of proteins](https://www.ebi.ac.uk/training/online/courses/biomacromolecular-structures/proteins/levels-of-protein-structure...primary/levels-of-protein-structure-secondary/) According to the above link: > Secondary structure refers to the regular, **local** structure of...the protein backbone, stabilized by intramolecular and sometimes intermolecular hydrogen bon…

protein-structure proteins

updated 2.1 years ago • user366312

count of similarity + identity +any gap not equal to the total number of sequences in results from local sequence alignment of protein? My query sequence was 249 long. The target is 3000 long. Local alignment only counted 241

protein alignment water sequence

updated 18 months ago • kng

Given a set of related protein sequences based on pairwise BLAST searches, how do I construct a multiple sequence alignment that contains only...and ignores unrelated parts of the input sequences? I assume this boils down to the problem of local multiple sequence alignment

local multiple protein sequence domain

updated 12.6 years ago • Christian

Hi, I have been given a task to compare the all the protein sequences of a strain of campylobacter with a strain of E.coli. I would like to do this locally using Biopython and

biopython blast

updated 10.2 years ago • satsurae

Dear all, I need to find locations of protein products of a certain list of genes. For example, TLR1(toll like receptor 1) locates on the cell membrane. Is there any...database can realize this goal? I know uniprot subcellular location. But it seems only 400+ genes are in the database. Is there any other database or any method I missed please

software error

updated 5.7 years ago • Yingzi Zhang

hi all, I need to pull out a specific protein from a transcriptome data deposited in a local server (using linux platform). I have the protein sequence in fasta. I...get to know from few papers that i need to use local blast and scan against all protein set. Can anyone tell me how to use unix bash scripting to pull out the protein from the

RNA-Seq blast

updated 8.2 years ago • ropni

Hi, I'm using signalp and targetp for subcellular localization. targetp presumably calls signalp for its secretory pathway prediction. "TargetP 1.1 predicts...Hi, I'm using signalp and targetp for subcellular localization. targetp presumably calls signalp for its secretory pathway prediction. "TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based…

protein

updated 12.1 years ago • Scg_Bio

Hey, I want to perform a GO term enrichment analysis by comparing a list of affected protein to all protein identified and/or genome. First I performed GO Slim mapper at SGD and then performed Fisher exact test...GO term individually. After doing all of that I realized I should probably have compared affected proteins to all proteins identified and not the the entire genome. I have noticed tha…

GO term enrichment DAVID GO Slim Bar graph Yeast

updated 8.0 years ago • Curie

to make analysis of my RNA-seq data and identify exact **isoform** function (biological process and subcellular localization). Is there any instrument for that? Thanks in advance

RNA-Seq isoform prediction

updated 6.9 years ago • Fill

Does anyone know how to build a local conserved domain database from multiple sequence alignment for running RPS-Blast locally? What I need to do is aligning...the protein sequence to those conserved domains to find the protein sequence with functional similarity. Can anyone help me

multiple-sequence-alignment blast RPS-BLAST

updated 11 months ago • BioPotato

Hi Has anybody used PLOP (Protein Local Optimization Program) to perform loop prediction. I want to predict the loop which is located between resi 42

protein-structure protein

updated 10.5 years ago • Reyhaneh

Like the question said. I am clueless. I have list of NLS (nuclear localization signal ) and list of proteins. I am interested to see whether any of my list proteins have my listed NLS

localization nuclear signal

updated 2.6 years ago • qmarulfiz

Hi, I recently start to use Pymol for protein protein interaction study. My protein candidates have co-expression profile (predicted by Genemania and String...and same localization; some of them contains shared protein domain. Then I created 3D structure pdb file of those proteins and loaded

sequence

updated 2.2 years ago • sw.arker

I have currently been using a local version of the BLAST nr database to run BLASTX to identify proteins but wanted to look into setting up a local version...speed up the time for processing our samples. NCBI however do not offer the clustered NR database locally and so wanted to ask if anyone knows the best way to go about setting up a clustered version of the nr database locally

diamond clustered-nr blast

updated 10 months ago • Wilford203

I've been having a ton of trouble trying to blastp my file of four protein sequences against a local database of protein sequences. I've been working on this for three days now using the BioPython...blast_handle = NcbiblastpCommandline(query='PATH/to/genes_of_interest.fasta', db='/PATH/to/local/db/protein.fa', out='PATH/to/results.xml') When I print blast_handle, I get this: blastp -out /PA…

BioPython blastp blast blast local database

updated 7.5 years ago • alissamariewilliams2015

of a fungal genome. Using OrthoMCL, orthologs within the four genomes (Well annotated and valid proteins) were obtained and functions were assigned. Later I ran the InterProScan and Pfam for further confirmations and...annotations. I have following questions: 1). I want to identify/count the KOGs in the generated protein sequences, I downloaded KOGs from ftp://ftp.ncbi.nih.gov/pub/COG/KOG/. Shou…

go kegg annotation

updated 11.2 years ago • Rahul Sharma

Hello, NCBI has an option to 'Align 2 or more sequences' in it's web portal for BLASTP (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&DATABASE=n/a&QUERY=&SUBJECTS=). As I understand, the main point of doing a local BLASTP is that it allows you to s…

blastp

updated 2.9 years ago • timothy.kirkwood

Hello, I am a beginner in bioinformatics and I want to use CPC to evaluate the protein coding potential of a transcript. To do this, I need to install the local blast package essentially 'formatdb'. I have

formatdb blast CPC

updated 2.3 years ago • Zac

remotely, but the server keeps logging me out. I think a better strategy would be to run BLAST+ locally with a database. I am performing protein BLAST alignment on chicken and mouse genes, so I would like to set up a local

BLAST R

updated 4.0 years ago • tom5

Hi everyone, I have a simple request: lets say we have 4 proteins. I know from several databases (Stitch, Uniprot, Etc..) that protein A binds directly to 3 different proteins (B, C, D), with...experimental evidences. If protein A has point mutation(s) or INDEL at known position(s), is there a way to predict its impact (Yes/No) on interaction with the...other proteins. I am not interested in th…

protein mutation

updated 10.5 years ago • Jean-Paul Abbuehl

m wondering how I can use commands like efetch, esearch, elink to get the necessary information from local databases. For example, here is a piece of code that I would like to do locally: system("esearch -db protein -query $inputGI...elink -target nuccore | efetch | xtract); the databases are downloaded locally, and I am aware of the SearchIO on Bioperl but I am very unsure how I can use th…

ncbi bioperl perl

updated 15 months ago • p6patel

Dear all, I have generated a database of protein sequences and selected a few sequences from it based on some criteria. Now I would like to model these selected sequences...and see if they folded into the native structure of a protein. The protein (native) shares a sequence similarity of 40% with all the sequences in the database. As I-tasser uses NR database...pdb to generate sequence profile …

3d-modelling blast software-error

updated 21 months ago • Neha shri

I often use `Jalview` for global alignment of proteins or DNA sequences for analyzing homologs, etc. However, I would like to be able to visualize many local alignments at...1 KB. I would like to be able to input the 20KB region and all 10 genes into Jalview, and conduct local alignments of each gene to the reference at once, so I can see where the genes are aligning to the gene region. Does anyo…

jalview

updated 21 months ago • JacobS

I want to do a local blast using all the bacterial protein data from NCBI. Is there any way to download all the data from NCBI

blast sequencing genome gene

updated 18 months ago • Eva_Maria

I want to do a local blast using all the bacterial protein data from NCBI instead of NR. Is there any way to download all the data from NCBI...Or to filter the NR database locally

parasite protein ncbi

updated 4.1 years ago • najibveto

I have a list of proteins that define a family of enzyme. I want to look if these enzymes are present in a genome I am working with. Therefore...approaches: blastp the above mentioned sequences against the genome create a hmm profile for the proteins and use hmmscan to search for them in the genome In both case I get a variable number of hits. However, there is something...that I am missi…

blast hmmer pfam proteins annotation

updated 9.2 years ago • dago

Can anyone manage to use the Mitoprot software locally for multiple protein sequences in a single file? The program can be downloaded from the links below but when I try to...run it on a multi-fasta file it seems to concatenate all the proteins sequences in the file, treating them as if they are one sequence, and gives just one output value. There's obviously

rna-seq genome software error

updated 7.0 years ago • wl284

I have been given a task to draw many protein domain structures. Considering the number of proteins, I think it would be necessary to do the work in batch. However...I couldn't find a proper tool. Is there a protein domain structure drawer (like the following one) that can be run locally? MyDomains

protein domain protein-structure

updated 10.4 years ago • sanchezcavani

I tried to use local psiblast but ran out of memory, and also tried 'https://webs.iiitd.edu.in/raghava/pfeature/pssm_profile1.php', but it...gave many missing values for several residues for a protein, so is there another way to calculate pssm for large batch of protein sequences

PSIBLAST BLAST PSSM MACHINELEARNING

updated 2.9 years ago • aakashy01

11,930 results • Page 1 of 239

Recent Votes

Answer: Heatmap and rna-seq

Answer: How to use limma to find differentially expressed genes in response to a continu

A: Blast Settings For Short Sequences

Comment: Heatmap and rna-seq

Answer: Heatmap and rna-seq

Comment: Heatmap and rna-seq

Recent Locations • All