Biostar

11,952 results • Page 2 of 240

the tool "KOBAS annotate" & "KOBAS identify". I would need help in setting up the field "BLAST protein database" since I don't understand how to configure it. I tried to download different fasta file from ftp://ftp.ncbi.nlm.nih.gov...of Galaxy in this field I used "NCBI NR (22 Jan 2018)" and I would like to use the same on my local installation. Thank you for the help

Galaxy KOBAS

updated 2.6 years ago • andrea.furlani

Hello Biostars, I am trying to search a customised HMM profile against the refseq protein databases using hmmsearch (HMMER 3.1b1) locally on my computer. I have performed a similar search against the UniProt...however, I am unable to find a similar option that allows me to filter the results obtained with local hmmsearch. Is it possible to filter results that match exact query architecture in t…

hmmer hmmsearch

updated 6.2 years ago • Sej Modha

I am trying to run a pblast locally. I have downloaded all the nr files from NCBI in a file with the following directory: '/home/lisa/Documents/nr' The first

alignment

updated 4.6 years ago • lisa96.barel

I want to create a local database using the ncbi database ftp files, am using clc main work bench to analyse my sequences (proteins), for some resean...I want to create a local database using the ncbi database ftp files, am using clc main work bench to analyse my sequences (proteins), for some resean it does not connect to the ncbi serve to download the ncbi through the software, so i decided to …

clc main workbench local database ncbi ftp files

updated 8.7 years ago • samuelksm

refseq_genomic` script to download human genomic datasets so that I can run the BLAST software locally. However, I realized these datasets would be for GRCh38 (the latest versions) and not GRCh37. 1. My question is to how to...get the files for GRCh37? 2. What command should I be using to run it locally. Since I will be aligning a chunk of different DNA sequences(query sequences could be up to 5…

genome blast alignment

updated 21 months ago • niharraul

I have some protein sequence and its id. How can I use them to generate pssm files? 1: From web site by perl 2: or by one program in my local pc ======================== for...to generate pssm files? Parsing web site by perl Get one program that can generate pssm file in local pc in Linux system

pssm perl

updated 12.7 years ago • Yu Hsiung

method might not work. So! I'm asking you if you have a better idea on how to get every bacterial protein sequence from NCBI. I don't think Edirect will work (I'll be blocked). One idea I had was if I could use esearch and efetch...on a local copy of the all protein record (nr.fa). However Edirect doesn't support local queries out of the box (at least to my knowledge...Any advice on how to wrang…

protein big data

updated 5.2 years ago • A Soggy Waffle

I have a set of 3 protein sequences for which I need to find the "consensus sequence" which can be used as an input to blast against a local database

blast

updated 13.7 years ago • Ananth

I am wondering if anyone knows how to download the entire human proteome including sub cellular localization information? https://www.uniprot.org/uniprotkb?facets=proteins_with%3A50%2Creviewed%3Atrue&query=Human

genomics

updated 16 months ago • Bioinfo

modifications (PTMs) of proteins, their subcellular location, and their biophysical characteristics in collaboration with UGent and UCL. We are...project by working towards a better understanding of the effect of PTMs (e.g. phosphorylation) on protein conformation and dynamics. This position will be highly collaborative, working with researchers at the Bio2Byte...and UCL, and will start with an e…

molecular-dynamics structural-bioinformatics

updated 11 months ago • Sergio Martínez Cuesta

Hi, How to download NCBI compiled protein database for specific genus ( eg. Acinetobacter baumannii) in a local computer

protein NCBI

updated 13 months ago • saadleeshehreen

sequences (formated as a fasta-file: >header \n sequence ...). I already translated them into proteins. I already made a local database of one of the files with the "makeblastdb" command. Now I would like to blast (blastp) every

blast command_line alignment sequence

updated 7.1 years ago • tmms

I want to blastp protein sequence file (>3000 sequences) against PDB database for generating templates for Homology modeling. Please help...I tried remote blast and local blast using formatdb but they are showing errors. Please help Thanks and Regards Money Gupta

blast

updated 2.3 years ago • money11gupta

Hi all! I was running local blast command for transcripts fasta sequences as below: blastx -query input/file.fasta -task blastx-fast -db blast-db...the last descriptions are all NA. My questions are: 1. How can I get organism name, description of protein ect. from list of accession numbers like WP_083411507.1, CBW15324.1. 2. I am observing that I have blast results for...pig protein whil…

blastx

updated 5.8 years ago • agata88

I have a list of a thousand residues identified on uniprot proteins. I need to gather features of these residues for a classifier. Some features require protein structures. I have a pipeline...for finding appropriate structures using the protein model portal, and calculating structure based features (pka, solvent accessibility, disorder, local charge, etc) using...would have rather used pre compu…

uniprot database

updated 9.8 years ago • samesense

Where can I find human protein data base for local blastx? I have already blasted my transcriptome against the nr database. My adviser wants me to...blast it against the human protein database and find out the genes named same way in both nr database and human database. I checked the ncbi ftp but couldn

blast human protein

updated 2.1 years ago • grayapply2009

Hi, I have several proteins datasets which I want to compare. I want to use sequence identity (not IDs) in order to count the number of shared proteins...between each dataset pair. I want to identify proteins which match perfectly and also proteins which are nearly identical (isoforms) and different proteins which are...highly similar over a large region of both proteins. So far, I have created…

blast comparison

updated 9.2 years ago • Kevin

Hello all, I am trying to establish a core proteome of A. baumannii, ie the proteins all of the strains have in common. I have multiple .fasta proteome files. What would be the most appropriate way of...Hello all, I am trying to establish a core proteome of A. baumannii, ie the proteins all of the strains have in common. I have multiple .fasta proteome files. What would be the most appropri…

blast blastp proteome core local

updated 4.0 years ago • zarodkip

I want local copies because I am trying to implement parallel blast using Apache Spark. I am choosing this particular domain, bioinformatics...options. I'm looking here: https://ftp.ncbi.nlm.nih.gov/ But can't figure out which one the protein database is. My plan was to download Sars-covid protein sequences and run Blast

ncbi blast

updated 16 months ago • nyck33

I have 2 protein sequences I need to compare using NCBI BLAST 1. the protein sequence as listed in a gbk file identified by the CDS 2. the...protein sequence that is translated from the nucleotide sequence denoted by the CDS location import sys import os from Bio

Biopython Python NCBI BLAST

updated 7.6 years ago • ahtmatrix

Hi mates, I was reading a paper which it states they identify protein sequences in *Halyomorpha halys* genome performing a local BLASTp search using the PFAM domain (PF00112) as **query** ([paper

proteome BLASTp

updated 16 months ago • Gerardo

Hello I wanted to know the name of the proteins encoded by a plasmid. For this, I am using blastp to blast the .faa file generated using Fraggenescan against the local

genome blast

updated 21 months ago • utkarsh.sood

I need to estimate the presence of some proteins in a group of bacteria (~100-200 species). I have their taxids and chromosome accessions. I don't want to do it manually...I need to estimate the presence of some proteins in a group of bacteria (~100-200 species). I have their taxids and chromosome accessions. I don't want to do it manually through the web blast and I decided to use blast+ and res…

proteins restriction BLAST

updated 2.9 years ago • Vasiliy Krestov

I am attempting to setup a local BLAST environment , and was doing some test queries on both the local blast environment and the online web server, when...were found in the web server results, but not the local results, are included in it. Specifically, I was test BLASTing this DNA Polymerase into humans, using the new taxids argument...putative DNA polymerase [Homo sapiens] 969 969 73% 0.0 97.…

BLAST

updated 4.9 years ago • jturner2

Hi, I want to do a local blast against a specific organism totally in-house without using negative gi list and remote option as the results...ways that I could think of even the custom db creation but the results differ because not all the proteins in my species I can get hold of through ncbi search as for some sequences a hit is found which doesn't come under the

blast

updated 2.1 years ago • Ritvik

Hi, I have a fasta file containing cDNA sequences and I would like to create a blastable database for blastplus, (using blastn) that I have installed locally. I am, however, unsuccessful up to now as I end up creating a PROTEIN database, although my file obviously contains DNA sequences. Here is the command I use, following blastplus user_manual.pdf: makeblastdb -in my_file.fasta -title my_…

blast makeblastdb

updated 4.6 years ago • Eric Normandeau

Hi everyone, Are there any softwares to do local realignment or local de novo assembly for the regions that users can specify arbitrarily, not just the regions near

software

updated 10.1 years ago • lyz10302012

Am trying to create a local database of bacterial protein, gene and genome sequences, these will be separate but i cannot find the bacterial ftp...file for the protein sequences, gene sequences, and genome sequences. does any one know the actual link to the download

blast

updated 7.2 years ago • samuelksm

Hello, I am creating a local table to convert from RefSeq protein identifiers (E.g,NP) to UniProt identifiers. RefSeq has a file named "gene_refseq_uniprotkb_collab.gz...quot; on their FTP server, which contains mappings from RefSeq protein to UniProt. However, there are 18 million mappings, and I want to build a table using only human identifiers. Is there

refseq uniprot human protein

updated 9.1 years ago • pwg46

for sequence alignment software used in pairwise sequence alignment , which can be used for ungapped local protein alignment with custom substitution matrix. I found out that in NCBI blastp there is -ungapped parameter but

local alignment blast substitution matrix

updated 8.0 years ago • cl10101

We have developed a method called [DMPfold][1] that predicts protein structures without templates using deep learning on sequence covariation data. It was applied to proteins in Pfam...25% of families without templates at high predicted accuracy. DMPfold can be downloaded and run locally under an open source license, and can also be run via the [PSIPRED web server][2]. It takes around 3 hours on…

deep-learning protein protein-structure

updated 10 months ago • jgreener

Henrik Nielsen,Vineet Thumuluri , José Juan Almagro Armenteros "DeepLoc 2.0: multi-label subcellular localization prediction using protein language models" Thursday 27 July, 19.00 (CET time) [Add to Google Calendar...Nucleic Acids Res. 2022 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9252801/) ). The prediction of protein subcellular localization is of great relevance for proteomics research. …

gene-ontology CAFA protein

updated 8 months ago • Alexander

Hello, Does anyone have any tips on how to do co-localization analyses on a handful of transcription factors? I see how to do everything up to peak-calling, but after that...Hello, Does anyone have any tips on how to do co-localization analyses on a handful of transcription factors? I see how to do everything up to peak-calling, but after that i...m not sure how I would go ahead analyzing co-lo…

Co-localization ChIPseq

updated 19 months ago • William

to know how I can do a blast against a database that I downloaded. I've downloaded a database of protein sequences from DEG (essential genes) and my idea is to do a blast against this database in my computer, using as input...a long list of proteins. The steps I performed so far were: 1) http://origin.tubic.org/deg/public/index.php/download (aminoacid sequence bacteria

makeblastdb

updated 2.7 years ago • BATMAN

Hi everyone , For exanple, full name or gene function description of PIN1 is "Serine/threonine-protein kinase PINK1, mitochondrial". It's subcellular location and papers already published with PIN1 shows that PIN1 plays

annotation gene

updated 2.4 years ago • Saber_J

Hello everybody, I need to obtain as much more as possible protein homology structures (.pdb) from a few hundred genes of Rattus norvegicus. Do someone know if is there a way to obtain...Hello everybody, I need to obtain as much more as possible protein homology structures (.pdb) from a few hundred genes of Rattus norvegicus. Do someone know if is there a way to obtain this...structures in an h…

tertiary protein high-throughput structure prediction

updated 2.9 years ago • francesco.costa.11

I have downloaded the Pfam-A database to find protein domains, but I'd like to add new domains that I have build with HMMER, but I don't know how to use both database together...For the new database, I have download the protein sequences in amino acids in a single fasta file, then I aligned the sequences with mafft and after that, I used the next

genome alignment gene

updated 5.4 years ago • erick_rc93

that happens quite often to me: I need to blast from 1,000 to 20,000 sequences in order to find the proteins these sequences code for. These sequences come from fish cDNA libraries, so I expect most of them, although not all...to code for proteins. I presently use 'blastplus' locally to query both swissprot and nr, but this approach is not so satisfactory for a few...but the ublast method cannot…

sequence blast software

updated 13.5 years ago • Eric Normandeau

which get timeout for long FASTA sequences . I have searched for solution and seems the local blast can solve it .However I could not able to find proper guidance on install it in the Ubuntu Machine . Is there a latest...specific resources that I can fallow to install local blast in Ubuntu Machine? It seems the Local Blast require large capacity and processing power .Is there any reference.…

blast local system requirement Ubuntu

updated 3.9 years ago • Kanchana Sankalpa

I need to query dbSNP locally, but I am puzzled with all the files I found on the ftp site. Can anyone guide me in this? which files should I download...I need to query dbSNP locally, but I am puzzled with all the files I found on the ftp site. Can anyone guide me in this? which files should I download in...order to query human snps? and are there tools already made to querying dbsnp locally? Ma…

dbsnp SNP

updated 8.0 years ago • tariktj

Omega of EBI and Blast of NCBI, both globally align sequences. Smith waterman of EBI align sequences locally, but work with just two sequences. I tried some other tools but they align globally. How can I align more than 2 sequences...locally

alignment local

updated 9.2 years ago • ehsansepahi

Hi! I have a list of bacterial genomes, and I want to find such common proteins from them, which can be found in ALL organisms (common would mean they match for at least 60%). What's the best way to do...Hi! I have a list of bacterial genomes, and I want to find such common proteins from them, which can be found in ALL organisms (common would mean they match for at least 60%). What's the best w…

blast alignment

updated 20 months ago • prostoesh

Hey, we are trying to get a local sub-part of dbSNP running on our servers here in our group. Since we are only interested in nsSNPs, we are specifically...Hey, we are trying to get a local sub-part of dbSNP running on our servers here in our group. Since we are only interested in nsSNPs, we are specifically interested in mappings of rs# to protein sequence, i.e. the concrete RefSeq identifier,…

dbsnp mapping protein snp

updated 8.1 years ago • Chris

I am attempting to perform a local blastp against the pre-indexed version of the entire protein nr database using an Ubuntu instance. The problem I am having...version of nr: sudo perl update_blastdb.pl --passive --decompress nr Searching nr with query protein fasta file: blastp -query /mnt/myquery.fasta -db /mnt/blastdb/nr -outfmt 6 -out ./myresults.out Where is the blastp command

protein blast nr

updated 13 months ago • katieostrouchov

Can anyone point me to a program [C/Python] that runs a Smith-Waterman pairwise local alignment but (unlike EMBOSS/water) has options for one or both of these: Return the best N hits of query sequence. Extend...the/each local alignment to produce the best full local alignment for the (much smaller) query sequence

pairwise sequence alignment

updated 13.1 years ago • Guidobot

Hello, I want to use Galaxy local to analyze my sequencing data of C. elegans. The most recent genome built for C. elegans is ce10, that is in Galaxy main, but...missing in my local instance. How to add a genome built to my local Galaxy? I am the admin on local Galaxy

galaxy

updated 21 months ago • meiemi2000

Hello is it possible to run blastX on a local database? If I download the entire database with update_blastdb.pl as shown [in this post][1], would blastX work? I need...Hello is it possible to run blastX on a local database? If I download the entire database with update_blastdb.pl as shown [in this post][1], would blastX work? I need to do this because in remote it takes too long to run. Locall…

sequencing alignment clustalX local database

updated 4.5 years ago • marongiu.luigi

Hi all , I have performed a local protein blast and it gave me an output which contains a lot of duplication . However, I sorted out the result w.r.t - e-value

blast

updated 7.2 years ago • namgyalwangstuklama

Hi all, when I run the following command for a local Blastp, I get no results returned even though there should be results. blastp -out /Users/Wes/Desktop/new_pairwise/blast.xml...Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs"", Nucleic Acids Res. 25:3389-3402. blastdb Query_1 gi|85676699|db…

alignment blast blastp

updated 3.1 years ago • weslfield

everyone, I'm new in bioinformatics field. I'd like to know how to and which are the best tools for local realignment around indels. I have fastq files coming from MiSeq (Illumina) as pipeline input and I'm performing the bioinformatic...pipeline using python (and running tools from comand line). I should perform local realignment only after PCR duplicates removal? And which tool should I use …

local realignment

updated 2.9 years ago • Elisa

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