Category: BLAST

the way to find pseudogenes in my scaffolds of genome

the way to find pseudogenes in my scaffolds of genome 3 Hello Recently, I assembled genome of a beetle living underground. My interest is searching pseudogenes (premature stop codon or frameshifts). I conducted tblastn using a few genes of model organisms (Tribolium) as query. But no premature stop codons were…

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KOBAS on Galaxy local

KOBAS on Galaxy local 0 Hello, I’m trying to setting up Galaxy on my PC. I need to use 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…

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Diamond and Taxonomic information

Diamond and Taxonomic information 0 Hello, I successfully executed the diamond makedb and blastx processes, and obtained the data file containing also the taxonomic information. Of course, I ran the makedb in the correct way, including the needed files: diamond makedb -p 4 –in /storage/RefSeq/small.nonredundant_protein.faa –taxonmap /storage/RefSeq/prot.accession2taxid –taxonnames /storage/RefSeq/names .dmp…

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Precision modeling of mitochondrial disease in rats via DdCBE-mediated mtDNA editing

Author Correction: Generation of somatic mitochondrial DNA-replaced cells for mitochondrial dysfunction treatment “ρ(-)”. Consequently, Figure 2(g) legend has been modified accordingly,. “MirCs were generated from mitochondrial disease patient-derived (7S) fibroblasts. (a) mtDNA CN during the procedure of MirC generation. Fibroblasts that received gene transfer, designated as 7S_ρ(-) were cultivated with…

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Blastx only uses one thread when word size is above 3

Blastx only uses one thread when word size is above 3 0 Hi all, I’m using blast version 2.12.0 and running the following command blastx -db my_db -query ecoli.fna -num_threads 8 -word_size 3 The query runs pretty fast and if I check the CPU usage is always around 600-700%. However,…

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How do I get description in BLAST?

How do I get description in BLAST? 0 Hi, all. I’m trying to get a description to the gene list using BLAST. I created the original database with the following command and did BLAST, but my output shows a lot of N/A. $ makeblastdb -in caenorhabditis_elegans.PRJNA13758.WBPS16.protein.fa -out elegansdb -dbtype prot…

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What is eggnog better than previous annotation in terms of?

What is eggnog better than previous annotation in terms of? 0 Hi, all. I used eggnog to get annotations in de novo RNAseq analysis But I haven’t understand the merit. What is eggnog better than previous annotation(ex. BLAST etc.) in terms of? Although I had read ths instruction in eggnog,…

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What is the best gun mod for GMOD?

[Top 10] Garrys Mod Best Weapon Addons Every Player Needs Customizable weaponry 2.0 – Khris’s Weapons – Full Package. No. Air To Surface Missile. RAMIREZ! … [TFA] Dead Space 2 Weapons. They’re coming out of the walls! … Tactical Baby Weapons. … WW2 Weapons Part 2. … Some throwable weapons….

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Restrict blastp search to set of specific species

Restrict blastp search to set of specific species 1 I want to perform a blastp search on a set of around 200 representative species with a list of known taxids. Is it possible using the web browser version of blast to efficiently limit my search without manually entering each of…

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Mitochondrial DNA leakage induces odontoblast inflammation via the cGAS-STING pathway

Dental caries are the most common health condition worldwide and can progress to pulpitis, a painful dental pulp infection. Odontoblasts at the pulp-dentin interface fight against these conditions by preventing bacterial invasion. In other pathological conditions, mitochondrial DNA (mtDNA)-related cell stress activates the cGAS-STING pathway, which contributes to inflammation, but…

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Diamond blastx: does it support SLURM?

Diamond blastx: does it support SLURM? 0 Hello, I have a cluster composed by 7 nodes (20 threads), running on SLURM (Ubuntu 20.04). I am trying to run the diamond blastx process on the cluster, but it just runs N-times the same process … Please, can someone tell me what…

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Learn Biopython: Preliminary Step Toward Bioinformatics

MP4 | Video: h264, 1280×720 | Audio: AAC, 44.1 KHz, 2 Ch Genre: eLearning | Language: English + .srt | Duration: 32 lectures (2h 28m) | Size: 815 MB Performing the Daily Tasks of Bioinformatics What you’ll learn: The basics of Python and Biopython Requirements There are no requirements except…

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Practical value of bits and SW-score in KEGG

Practical value of bits and SW-score in KEGG 1 Hello, Can someone explain to me the practical value of bits and SW-score in KEGG? What does it actually mean for my sequence? The image below shows paralogs table as shown in the base what is the practical value of these…

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Plot Blastn.table file on R

Hi I’m trying to find a way to plot the results of my blastn script (.table output file). The output file is quite big since I had to characterize more than 200 gRNA target sites. The file contains also a lot of duplicated hits on the subject column and i…

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BLAST Results, location on genome

BLAST Results, location on genome 0 Hi, I’m visualizing a genome, and i have to be able to get from a blast search result to the location of the hit. So im running a BLAST instance locally, and I already generated a BLAST db. Searching against this db works, but…

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Gene Editing Facility | CRISPR | Cas9

The iPSC Derivation & Gene Editing Core is a facility established and managed by the MCRI Stem Cell Medicine Initiative and has been in operation since 2014. This facility brings together a team of highly experienced stem cell and molecular biologists with over 40 years combined experience to generate standard and gene-edited iPSC…

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NGSeq/DHPGIndex: This tool is for compressing and indexing pan-genomes and genome sequence collections for scalable sequence and read alignment purposes.

General This tool is for compressing and indexing pan-genomes and genome sequence collections for scalable sequence and read alignment purposes. The pipeline can be deployed in cloud computing environment or in dedicated computing cluster. The tool extends the CHIC aligner gitlab.com/dvalenzu/CHIC with distributed and scalable features. DHPGIndex have been tested…

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Protein Sequences MSA vs. BLASTp

Protein Sequences MSA vs. BLASTp 0 Hello everyone here! I am recently working on ligand discovery. What I’m doing now is to find out if the ligand which targets the pathogen’s specific enzyme will also have effect on human’s. I do BLAST to pathogen’s protein to look for similar proteins…

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FGFR2 inhibitors in intrahepatic cholangiocarcinoma

Massimiliano Salati,1,2 Francesco Caputo,1 Cinzia Baldessari,1 Pietro Carotenuto,3 Marco Messina,4 Stefania Caramaschi,5 Massimo Dominici,1 Luca Reggiani Bonetti5 1Department of Oncology and Hematology, University Hospital of Modena, Modena, Italy; 2PhD Program Clinical and Experimental Medicine, University of Modena and Reggio Emilia, Modena, Italy; 3Department of Genomics, Telethon Institute of Genetics and…

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Summary of KEGG functional categories from an annotated genome? Is there a tool for this?

Summary of KEGG functional categories from an annotated genome? Is there a tool for this? 0 I have several annotated bacterial genomes that I have been analyzing. I have run them through the web-browser utility BlastKOALA to get KEGG functional annotations. This generates a list of KO numbers and allows…

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Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits

Significance Marine dissolved organic matter, which originates from phytoplankton, holds as much carbon as Earth’s atmosphere; yet, the biological processes governing its fate are primarily studied under idealized laboratory conditions or through indirect measures such as genome sequencing. In this work, we used isotope labeling to directly quantify uptake of…

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Tumor Biology Lab Research Associate Job at UC San Diego Health

– Advertisement – Tumour Biology Lab Research Associate Job at UC San Diego Health Filing Deadline: Mon 10/18/2021 For the safety and well-being of the entire university community, the University of California requires, with few exceptions, that all students, faculty and staff be vaccinated against the COVID-19 virus before they…

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The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests

Sequencing of Shorea leprosula genome Sample collection Leaf samples of S. leprosula were obtained from a reproductively mature (diameter at breast height, 50 cm) diploid tree B1_19 (DNA ID 214) grown in the Dipterocarp Arboretum, Forest Research Institute Malaysia (FRIM). DNA extraction Genomic DNA was extracted from leaf samples using the…

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Intercellular transfer of mitochondrial DNA carrying metastasis-enhancing pathogenic mutations from high- to low-metastatic tumor cells and stromal cells via extracellular vesicles | BMC Molecular and Cell Biology

Reagents GW4869, a neutral sphingomyelinase inhibitor, and tipifarnib, a farnesyl transferase inhibitor, were obtained from Cayman Chemical (Ann Arbor, MI, USA) and ChemScene LLC (Monmouth, NJ, USA), respectively. MitoTracker Red CMXRos, MitoTracker Deep Red FM (MTDR) and CellLight mitochondria-GFP (mtGFP) were supplied by Thermo Fisher Scientific (Waltham, MA, USA). MitoBright…

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Blast applications analysis at MainKeys

add to compare Best Penny Stock, Best SEO Company New York, Marketing Company New York blastapplications.com Blastapplications is one of the largest Best Penny Stock New York, Best SEO Company New York, Marketing Company New York best seo company new York. And much more. 0  add to compare InvestorsHub –…

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filtering results by a minimum % of identity and % coverage

BLASTp command line : filtering results by a minimum % of identity and % coverage 0 Hi all, I use regularly BLASTp analysis and I would like to improve my command line so that only resulting hits with 60% of similarity and 60 % of coverage appear in the output…

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Generation of knock-in lampreys by CRISPR-Cas9-mediated genome engineering

Strategy for generating knock-in lampreys with the LcHsp70A promoter For CRISPR-Cas9-mediated knock-in via non-homologous end joining (NHEJ) in the lamprey, we used an experimental strategy previously established in zebrafish13 and medaka14 with minor modification: co-injection of sgRNA1 (for genome digestion), sgRNA2 (for plasmid digestion), donor plasmids, Cas9 mRNA, and fast…

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Cell reprogramming shapes the mitochondrial DNA landscape.

dc.contributor.author Wei, Wei dc.contributor.author Gaffney, Daniel J dc.contributor.author Chinnery, Patrick F dc.date.accessioned 2021-10-05T00:26:36Z dc.date.available 2021-10-05T00:26:36Z dc.date.issued 2021-09-02 dc.identifier.issn 2041-1723 dc.identifier.other 34475388 dc.identifier.other PMC8413449 dc.identifier.uri www.repository.cam.ac.uk/handle/1810/328995 dc.description.abstract Individual induced pluripotent stem cells (iPSCs) show considerable phenotypic heterogeneity, but the reasons for this are not fully understood. Comprehensively analysing the mitochondrial genome…

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Gitelman-Like Syndrome Caused by Pathogenic Variants in mtDNA

This article was originally published here J Am Soc Nephrol. 2021 Oct 4:ASN.2021050596. doi: 10.1681/ASN.2021050596. Online ahead of print. ABSTRACT Background: Gitelman syndrome (GS) is the most frequent hereditary salt-losing tubulopathy characterized by hypokalemic alkalosis and hypomagnesemia. GS is caused by biallelic pathogenic variants in SLC12A3, encoding the Na+-Cl– cotransporter…

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Quantitative PCR assay for detection of Helicobacter pylori

Introduction Helicobacter pylori is a common pathogen that infects nearly 50% of the global population.1 Infection with this pathogen causes chronic gastritis, which can cause chronic gastroduodenal diseases such as gastritis, gastric ulcer, duodenal ulcer, gastric cancer, and gastric mucosa-associated lymphoid tissue (MALT) B-cell lymphoma.2 Although H. pylori is the…

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Gmod Vj Cars

Jan 13, 2008 · As “Gmod N” A map of groups ˚ (G 1;) !(G 2;1312 · Garry’s Mod Store Page Garry’s Mod > Workshop > Hoodwink abuser’s Workshop This item has been removed from the community because it violates Steam Community & Content Guidelines It is only visible to you…

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How To Extract A Sequence From A Big (6Gb) Multifasta File ?

How To Extract A Sequence From A Big (6Gb) Multifasta File ? 11 I want to extract some sequences using ID from a multifasta file. Using perl is not possible because it gave an error when indexing the database. Maybe because of it’s size? Is there any way to this…

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Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens

Significance The molecular mechanisms underlying pigmentation patterns in animals is to a large extent an unresolved mystery in biology. For example, compared with mammals, birds show a stunning diversity in pigmentation patterns. This study advances the knowledge concerning the mechanisms creating periodic pigmentation patterns in individual feathers. We show that…

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Inferring homology from BLAST scores/statistics : bioinformatics

Hello, I have some proteins with blast homologs, and I am trying to get a quantitative measure of the representativeness of each match. As I understand, everyone normally compares blast alignments using bit scores, as these are database-size independent. However (please correct me if I’m wrong) bit-scores only describe the…

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Inferring homology from BLAST scores/statistics

Inferring homology from BLAST scores/statistics 0 Hello, I have some proteins with blast homologs, and I am trying to get a quantitative measure of the representativeness of each match. As I understand, everyone normally compares blast alignments using bit scores, as these are database-size independent. However (please correct me if…

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Postdoc- Epigenetics in cellular plasticity and drug resistance of neuroblastoma

Category Research / Academic Location Amsterdam We are offering a research position for a highly motivated Postdoc to study the epigenetic differences in neuroblastoma. Neuroblastoma is a pediatric tumor with often a fatal outcome. Primary tumors go in complete remission upon therapy, but relapse as resistant disease. At the department…

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Research Assistant in Genomics / Bioinformatics Jobs at Nutrition Technologies , Singapore

Less than a year of experience Important Information Make sure you’re applying to a legit company by checking their website and job posts. Job description Research Assistant in Genomics / Bioinformatics Nutrition Technologies Nutrition Technologies is an innovative company producing insects as a sustainable protein source for the animal feed…

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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…

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Blast Portal – LoginWave

If you are looking for blast portal, simply check out our links below : blast.ncbi.nlm.nih.gov/The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to … blastconnect.com/ Blast Connect is an information analysis, reporting, player management, and coaching application for…

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How to make BLASTN be aware of short read?

I’m using blastn (anaconda.org/bioconda/blast) to find similar sequences of a target sequence against a FASTA file. But my read is quite short (68 bases). I realised that blastn won’t report any hit. But there is actually a very good one in the FASTA file after checking manually. Here is the…

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Decreased mitochondrial DNA copy number in nerve cells and the hippocampus during nicotine exposure is mediated by autophagy

doi.org/10.1016/j.ecoenv.2021.112831Get rights and content Highlights • Long-term nicotine exposure induces detrimental effects on mitochondria. • Markedly lower mtDNA copy number is a potential biomarker of nicotine addiction. • Decreased mtDNA copy number induced by nicotine is mediated by autophagy. Abstract Cigarette smoke is a harmful air pollutant and nicotine dependence…

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Are BLAST search parameters recorded in the XML file?

Are BLAST search parameters recorded in the XML file? 1 Hi, I have XML files from BLASTn searches but I’m not sure what, if any, parameters were selected. Would this be recorded in the file? I’m specifically interested in if a different “Max target sequences” was selected. How might I…

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Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach

Genome assembly In this study, we de novo assembled the plum, Prunus mira, and Prunus davidiana genomes for the first time and improved the peach and apricot genomes by integrating single-molecule real-time (SMRT) long-read sequencing (PacBio), short high-quality Illumina paired-end sequencing, and Hi-C technology. First, we used SMRT reads (99−130 Gb,…

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Mutational profile of the dystrophin gene

Introduction Duchenne Muscular Dystrophy (DMD-OMIM #310200) and Becker Muscular Dystrophy (BMD-OMIM #300376), are the most common hereditary muscular dystrophies around the world.1 DMD and BMD occur with a frequency of 1/3.300 and 1/6.000 newborn males, respectively.2 These dystrophinopathies are caused by alterations in the DMD gene and have an X-linked…

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Unraveling the hidden role of a uORF-encoded peptide as a kinase inhibitor of PKCs

Short open reading frames (ORF) upstream of the canonical ORF (uORFs) are found in about 40% of human protein-coding transcripts (1⇓–3). uORF-containing genes were shown to participate in heavily regulated processes, including differentiation, cell cycle control, and stress responses (4⇓–6). Ribosome profiling data revealed that many uORFs are translated (3,…

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Is there really a difference in blastn -task blastn and -task megablast when dealing with unmapped reads?

Forum:Is there really a difference in blastn -task blastn and -task megablast when dealing with unmapped reads? 0 Hi all, I’ve been running a variety of blastn options with my metagenomic dataset with the goal of trying to find the best hits for my contigs (produced from metaspades). I’ve recently…

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Vero cell-adapted Infectious Bursal Disease virus LC-75

Introduction Infectious bursal disease (IBD), also known as Gumboro, is an immunosuppressive disease of chickens and is the second priority chicken disease in Ethiopia, next to Newcastle disease, that needs to be controlled primarily through vaccination.1 The etiological agent is IBD virus (IBDV) which belongs to the family Birnaviridae, a…

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Unusual FastQC sequence distribution from small RNA seq

Unusual FastQC sequence distribution from small RNA seq 0 Hi, I am attempting to analyse some small RNA sequencing data produced using an Illumina TruSeq Small RNA Library Preparation Kit. The RNA was isolated from sheep serum. Pre-sequencing QC was fine and post sequencing looked good too – apart from…

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Pathway Hole Filler

Pathway Hole Filler 0 Hello, I am using Pathway Tools v 25.0 and I am trying to run the Pathway Hole filler on my database. However, each time I tried to run it, the hole filler failed. I got the error message: PathoLogic is unable to prepare BLAST protein data….

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install biopython jupyter

like BLAST, ClustalW, FASTA, GenBank, PubMed ExPASy, SwissProt, and many more. conda install-c conda-forge ipyleaflet With pip: pip install ipyleaflet If you are using the classic Jupyter Notebook >> import Bio >>> Bio.__version__. For Windows we provide click-and-run installers. The easiest way to install statsmodels is to install it as…

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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,…

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genbank submission tutorial

These are just a few of the questions answered in this comprehensive overview of Bayesian approaches to phylogenetics. Finally, make sure the Include Primers box is unchecked, as we are not submitting primers with this sequence. Influenza virus sequences. September, 2008. Please download the current version. Some mitochondrial genomes contain CDS’s that…

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The next frontier for human embryo research

A mouse embryo cultured until day 11.Credit: Weizmann Inst. In a laboratory in Israel, an incubator drum spins on a bench. The two glass bottles attached to the drum contain mouse embryos, each the size of a grain of rice, with translucent, pulsing hearts. Whole mouse embryos have typically been…

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Shining a light on extrachromosomal DNA

In 2021, Stanford ChEM-H welcomed physician scientist Paul Mischel, professor of pathology, as an Institute Scholar. Mischel has pioneered the field of extrachromosomal DNA (ecDNA), circles of genes that float outside chromosomes, the well-organized home for genes in healthy cells. These long-overlooked structures, present in an estimated up to one-third…

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How to verify putative miRNA

How to verify putative miRNA 1 My PI gave me a list of some DNA sequences, each one around 25 nucleotides, that are suspected to code for Vitis Vitinesfera miRNA. To know if they are complementary to some mRNA for a known protein sequence, we do the following process: BLAST…

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How do you get the result of BLAST like this paper?

Since you’re blasting with ncbi-NR you’re almost there. By changing the blastx output options to outfmt 6 you’re receiving tabular output in avenae.out, you can customise the output columns to also receive the species names. For example, you could run: blastx -query /home/nkarim/avenae/trinity_even_out_dir/Trinity.300.longest.fasta -db /home/nkarim/blast/db/nr -outfmt “6 qseqid sseqid sscinames…

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genomic data scientist jobs

Provide strategic planning and perform analysis or simulations independently or in a . 401(k) savings plan match.…, Requires a Ph.D. in Biochemistry, Biotechnology, Molecular/Cell Biology, Plant Biology, or a related field and 0-3 years of relevant postdoctoral or industrial……, In addition, the analyst will help advance the groups collective expertise…

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entry level bioinformatics jobs near me

Indeed ranks Job Ads based on a combination of employer bids and relevance, such as your search terms and other activity on Indeed. computer science, information science, Candidates should be interested in innovative, interdisciplinary approaches to modeling mammalian physiology and disease using approaches in data science,…. Sign up with Facebook….

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bioinformatician jobs

1 The first category includes developers who implement algorithms and develop tools for bioinformatics. Simply put, it has just the right breadth and depth, and it reads well. In fact, readability is one of its virtues—making the book enticing and useful, all at once…” Human Vaccines, 2010 “… This book…

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Subsetting Common Differentially Expressed Genes in Multigrade Glioma

Subsetting Common Differentially Expressed Genes in Multigrade Glioma 0 Hello! So I am working on reconstructing a gene regulatory network for Glioma/Glioblastoma starting from RNA-seq data. the data I have is for different patients at different stages of the disease (different grades 2, 3 and 4). I ran a differential…

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Blood test may predict response to CAR T-cell therapy

September 28, 2021 3 min read Source/Disclosures Published by: Disclosures: Miklos reports consultant/advisory roles with Adaptive Biotechnologies and Kite Pharma/Gilead Sciences. Please see the study for all other authors’ relevant financial disclosures. ADD TOPIC TO EMAIL ALERTS Receive an email when new…

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bioinformatics analyst entry level

The average bioinformatics analyst salary is $71,298 per year, or $34.28 per hour, in the United States. $12.75 – $24.25. Bioinformatics Analyst. Jobs Limited to Sustainable Energy. Proficiency in programming in C, C++, C#, or Java. Create more job alerts for related jobs with one click: Junior to Mid-level Patent…

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genbank database slideshare

Found inside – Page iiThis book describes the historical importance of potato (Solanum tuberosum L.),potato genetic resources and stocks (including S. tuberosum group Phureja DM1-3 516 R44, a unique doubled monoploid homozygous line) used for potato genome … If you continue browsing the site, you agree to the use of…

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genbank submission bankit

Submission of sequence data to NCBI archives . Learn more. This post will show you how to… Careers, General: your contact details, authors, publication, data release date, Original or third-party assembly/annotation, Set designation (if applicable) for multiple sequences of the same locus, Nucleotide sequences in FASTA or alignment format, Source…

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biopython extract sequence from fasta

My two questions are: What is the simplest way to do this? This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. using python-bloom-filter, just replace the set with seen = BloomFilter(max_elements=10000, error_rate=0.001). This book is suitable for use as a classroom textbook,…

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ncbi genbank submission

This document describes how to use the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus command line interface of the GenBank Submission Portal. Found inside – Page 4NCBI builds GenBank primarily from the submission of sequence data from authors and from the bulk submission of expressed sequence tag (EST), genome…

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rs2507799 was found to be linked with increased risk for IS

Introduction Ischemic stroke (IS) is caused by the sudden loss of blood circulation to an area of the brain that causes injury to neurological function and represents a major cause of global disability and mortality.1 IS is known to be a heterogeneous and multifactorial disease. Genetic factors, particularly those involving…

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Error message running GeMoMa

Error message running GeMoMa 0 I am trying to run GeMoMa for gene annotation using RNA-seq evidence. java -jar -Xms25G -Xmx50G GeMoMa-1.6.1.jar CLI GeMoMaPipeline t=target.fasta s=own a=ref-annotation.gff g=ref.fa outdir=test r=MAPPED ERE.s=FR_UNSTRANDED ERE.m=target-accepted_hits.bam ERE.v=SILENT ERE.c=true tblastn=true Extractor.p=true Extractor.r=true Extractor.s=true Extractor.f=true AnnotationFinalizer.u=YES AnnotationFinalizer.r=NO p=true pc=true pgr=true However, I am getting this error…

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blast culling_limit option behavior

blast culling_limit option behavior 0 I am using culling_limit 1 as a parameter From the manual : Delete a hit that is enveloped by at least this many higher-scoring hits My understanding : The culling limit can be used to remove redundant hits. In practice it sets the number of…

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How to download BLAST+ on Centos (6)

How to download BLAST+ on Centos (6) 1 Hi How to start with installing and downloading NCBI BLAST+ on my Centos? Steps to follow replies will be helpful Thank you Centos BLAST • 295 views I don’t know which version of Centos you have, but try with Bioconda. Unless your…

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Genetics lab using genbank blast search – Freelance Job in Physical Sciences – $10 Fixed Price, posted September 25, 2021

What is GenBank? ​GenBank is an international database of DNA, RNA, and protein sequences.  Basically, whenever someone sequences a molecule, he or she deposits the sequence in GenBank.  GenBank is run by NCBI (National Center for Biotechnology Information).  NCBI is an organization that maintains several molecular databases (including GenBank) that are mostly focused…

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Temas para TCC Point Mutations of the mtDNA Control Region in Normal and Neurodegenerative Human Brains

Point Mutations of the mtDNA Control Region in Normal and Neurodegenerative Human Brains AUTOR(ES) Chinnery, P. F. FONTE The American Society of Human Genetics RESUMO Recent observations in cultured human fibroblasts suggest that the accumulation of point mutations in the noncoding control region of mtDNA may be important in human…

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The BLAST command stops with an error.

The BLAST command stops with an error. 0 Hi all. I would like to evaluate the assembly quality by running BLAST to the fasta file output by Trinity. I ran the command as follows, but this job was stopped with an error message. $ ~/miniconda3/envs/py27/bin/blastx -query /home/nkarim/avenae/trinity_even_out_dir/Trinity.300.longest.fasta -db /home/nkarim/blast/db/nr -outfmt…

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Bioinformatics tutor for homework help (Introductory level) – Freelance Job in Quantitative Analysis – Less than 30 hrs/week – 1 to 3 months

I am taking a graduate level course in Bioinformatics and need tutor help with topics such as: – sequence alignment – dot plots – BLAST The goal is to go through assignments together to understand concepts. This job will include meetings and chat. Hourly Project Length Duration I am willing…

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Is there a way to make the BLAST results easier to read?

Is there a way to make the BLAST results easier to read? 1 Hi all. I’m trying to get assembly stat. As part of that, I would like to evaluate the assembly quality by running BLAST to the fasta file output by Trinity. I got the result by blastx, but…

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Effects of electroporation on anticancer activity of 5-FU and newly synthesized zinc(II) complex in chemotherapy-resistance human brain tumor cells

. 2021 Sep 22;38(11):129. doi: 10.1007/s12032-021-01579-7. Affiliations Expand Affiliations 1 Department of Occupational Health and Safety, Faculty of Health Sciences, Muş Alparslan University, 49250, Muş, Turkey. me.alkis@alparslan.edu.tr. 2 Department of Chemistry, Faculty of Arts and Sciences, Muş Alparslan University, 49250, Muş, Turkey. 3 Department of Molecular Biology, Faculty of Arts…

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act comparaison of 2 genomes

act comparaison of 2 genomes – problem with the blast output 1 Hello, I don’t know if any of you came across that problem before but when I do a blast of one genome against a database (with the 2nd genome) I get a blast against only one of the…

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act comparaison of 2 genomes

act comparaison of 2 genomes – problem with the blast output 1 Hello, I don’t know if any of you came across that problem before but when I do a blast of one genome against a database (with the 2nd genome) I get a blast against only one of the…

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Error: mdb_env_open: Bad file descriptor

Error: mdb_env_open: Bad file descriptor 0 Hi, I am trying to use the following command: blastn -task blastn -db blastdb/nt/nt -query genome_bin.1.fa -out genome1.out and I am facing the following error: Error: mdb_env_open: Bad file descriptor I am not able to find anything regarding the same. It will be really…

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Makeblastdb error: file does not exist.

Makeblastdb error: file does not exist. 0 I just downloaded the blast command line applications and I would like to make a database of a MGEs nucleutides that i downloaded from ACLAME database site in fasta file. It is labeled as mydb.fasta and I have put the file into a…

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Gromacs mdp options 2019

Gromacs mdp options 2019 Revision History | Winmostar(TM)LATEST PERFORMANCE ENHANCEMENTS TO GROMACS ON …g_mmpbsa Mailing List – Google Groups I was ready to marry her on the first date, but I also have two classes this morning, pushing aside the fear…

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Blast Algorithm – Subject:- Bioinformatics BLAST Algorithm Introduction BLAST identifies homologous

Preview text Subject:- Bioinformatics BLAST Algorithm Introduction BLAST identifies homologous sequences using a heuristic method which initially finds short matches between two sequences; thus, the method does not take the entire sequence space into account. After initial match, BLAST attempts to start local alignments from these initial matches. This also…

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Is it possible to isolate and merge overlapping hits from a BLAST search Aligned Fasta file?

Hello all, Hope you’re well. I started a PhD in Jan this year and frankly I am struggling. I’m coming into the second week of trying to figure out how to attempt this problem and it’s honestly starting to get to me a bit – the current task I’m working…

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Ttc30a affects tubulin modifications in a model for ciliary chondrodysplasia with polycystic kidney disease

Significance Cilia are tubulin-based cellular appendages, and their dysfunction has been linked to a variety of genetic diseases. Ciliary chondrodysplasia is one such condition that can co-occur with cystic kidney disease and other organ manifestations. We modeled skeletal ciliopathies by mutating two established disease genes in Xenopus tropicalis frogs. Bioinformatic…

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Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering

Annual and perennial species occur in many plant families. Annual plants and some perennials are monocarpic (flowering once in their life cycle), characterized by a massive flowering and typically produce many seeds before the whole plant senesces. By contrast, most perennials live for many years, show delayed reproduction, and are…

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command for isolate unique reads with unique subject id

command for isolate unique reads with unique subject id 0 So as you see below there is 1 file that contains a different column. So as some reads are multiple align to different subject id, so I want to isolate only one read which contains the highest bit score but…

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BLAST multiple sequences against each other from one FASTA file

BLAST multiple sequences against each other from one FASTA file 1 Hi, I am a beginner to using BLAST locally on Mac OSX. I have downloaded ncbi-blast-2.2.31+.dmg and have installed it. I have a FASTA file with multiple protein sequences in it and am trying to BLAST each sequence against…

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What does it mean BLASTx in de novo RNAseq analysis?

What does it mean BLASTx in de novo RNAseq analysis? 1 Hi, all. I try to get an assembly stat. According to some articles, it tends to have information that can be obtained by BLAST. For example, “Top BLASTx-hit species” and “Percent of gene with at least one BLASTx hit…

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BLAST Annotating Sub-sequences of Features with Not Normalized Identity Scores

BLAST Annotating Sub-sequences of Features with Not Normalized Identity Scores 1 I’m using BLAST annotation to annotate protein features using the online tool Below is a screenshot of the entered queries. Below is a screenshot of the result. My question is there is a parameter to let BLAST normalizes the…

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MGEs analysis in metagenomic data by ACLAME data base

MGEs analysis in metagenomic data by ACLAME data base 0 Hello everyone. I want to analyze MGEs from metagenomic data and i already trimmed adaptors sequences by scythe and trimmomatic and got my clipped fasta file. I want to analyze MGEs by ACLAME database. For that i need your guideline…

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hypothetical protein DAPPUDRAFT_213302, maker-scaffold2255_size18018-snap-gene-0.6 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of hypothetical protein DAPPUDRAFT_213302 vs. L. salmonis genes Match: EMLSAG00000000401 (supercontig:LSalAtl2s:LSalAtl2s1063:86108:87342:-1 gene:EMLSAG00000000401 transcript:EMLSAT00000000401 description:”maker-LSalAtl2s1063-snap-gene-0.46″) HSP 1 Score: 149.443 bits (376), Expect = 4.121e-44Identity = 91/196 (46.43%), Postives = 119/196 (60.71%), Query Frame = 0 Query: 14 MDKITDLQVEPLT–NSRFVKPLRLRFKQDGKVKVWDLIQCHASVAVVIFNQTTQKFVFVRQFRPAVYFSALRRAQGDVEPGTQFKGDEIDPKVGITLELCAGIVD-KSKSLIEIAHEEILEETGYDVPMNLIEEIQTFPVGVGVGGENMTLFCAEVTEAMRKGPGGGLAEEGEMIDVIEMGVEETRTLMRAKSVT 206 MDK+ VEPL +SRFV P R+ ++Q+G…

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Biopython Contact Us | Contact Information Finder

Listing Results Biopython Contact Us Biopython · Biopython 2 hours ago Biopython.org View All Biopython. See also our News feed and Twitter. Introduction. Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.. It is a distributed collaborative effort to…

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Transcriptome assembly, annotation and submission to GenBank for unannotated organisms

Monday, October 4 at 3:00pm to 4:00pm Virtual Event Transcriptome assembly and annotation is a complex process that requires the integration of multiple databases using several computational tools for best results. The advances in next-generation sequencing technologies and the decrease in the cost of sequencing a complete transcriptome are driving…

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Can you BLAST on specific sequences? : bioinformatics

Hi all, noob MSc here. I want to confirm the knockdown targets of my siRNAs (i.e. check an siRNA knocks down more than one transcript variant) I’d like to find an efficient method. Method #1: CTRL+F my siRNA sequence on the FASTA mRNA sequence Con: this only allows for 100%…

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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…

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Submit sequence data to NCBI

Data provision and standards. GEO sequence submission procedures are designed to encourage provision of MINSEQE elements: Thorough descriptions of the biological samples under investigation, and procedures to which they were subjected. Thorough descriptions of the protocols used to generate and process the data. Request updates to accessioned records per the…

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Characterization and expression of DNA sequences encoding the growth hormone gene in African Pygmy Mouse (Mus minutoides)

Abstract We determined the nucleotide sequence of the growth hormone (Gh) gene in Mus minutoides, one of the smallest mammals, where was predicted to be distinct in the functional regions between M. minutoides and Mus musculus. To investigate the evolutionary characteristics of Gh in M. minutoides, we constructed a phylogenetic…

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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….

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GRRDUser Manual [PDF] | Documents Community Sharing

* The preview only display some random pages of manuals. You can download full content via the form below. Microsoft Word Add-In for the GenePattern Reproducible Research Document July 2009 Introduction…………………………………………………………………………………………………………………. 3 About GenePattern…………………………………………………………………………………………………… 3 How GenePattern and the GRRD Add-In Work Together…………………………………………………4 Reproducibility of Document Interactions………………………………………………………………………4 Installing and Uninstalling…

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How to download all the genome fasta file for plants?

How to download all the genome fasta file for plants? 1 Hello, I want to download all genome fasta file of plants from NCBI for executing stand alone blast. Please share any command line tools are available. Thank you Mathavan M standalone blast • 68 views NCBI Datasets is specifically…

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