Tag: msa

PRESS RELEASE Published June 2, 2023 As per the study initiated by Evolve Business Intelligence, the global Radio Headset market size accounted for USD 4.5 Billion in 2022, growing at a CAGR of 6.1% from 2023 to 2033. Radio headsets are designed to provide reliable and efficient communication in demanding…

Abstract De novo protein design enhances our understanding of the principles that govern protein folding and interactions, and has the potential to revolutionize biotechnology through the engineering of novel protein functionalities. Despite recent progress in computational design strategies, de novo design of protein structures remains challenging, given the vast size…

I’ll follow up what a few others have mentioned, but I like stats.sh within the BBTools package for raw assembly stats. I’ll then polish my assembly and pare it down to the targeted contigs (eg. those annotated as bacteria/viruses/your genome of interest/etc.) then I like to use quast/metaquast to evaluate…

Considering gaps in calculating conservation score from MSA 0 Dear all, I was looking for a good way to calculate conservation scores over columns in an MSA. I usually use Kullback-Leibler-Divergence (kl_divergence) or Shannon entropy. However, I would like to know if it makes sense to penalize gaps, when calculating…

During a particular baseball trout, 8 baseball players were given 40 pitches each. Of each player’s 40 pitches, 20 pitches came from left-handed pitchers and 20 came from right-handed pitchers. Of the 20 pitches that each player saw from each of the pitchers, 10 pitches were curve balls and 10…

Vector construction The Cas9/sgRNA vector (all-in-one) (GenBank accession no. OQ579018) contained sgRNA and Cas9-2A-mCherry expression cassettes. The sgRNA (5′-ATGCAGAACTAGAGTACAGC-3′) targets the phiC31 pseudo-attP intergenic site located on chromosome 3 of CHO-K1 genome (GenBank accession no. APMK01032147.1) (Fig. 1a). To construct the Cas9-mSA/sgRNA vector (GenBank accession no. OQ579019), the monomeric streptavidin (mSA)…

Identifying Mutation Frequency Changes in MSAs over time? 0 Hello, I have 6 sample fasta files total over 3 time points: WEEK 3, 5 & 7. There are two samples per time-point which are Control and Positive for a Specific Gene. These samples are YU2 HIV viral transcriptomes. In each…

Plant material Bread wheat accessions Transfer (TA5524), WL711, TA5605, Ae. umbellulata accession TA1851 and Ae. triuncialis accession TA10438 were obtained from the Wheat Genetics Resource Center (WGRC). TcLr9 (Transfer/6*Thatcher) is a near-isogenic line carrying Lr9 from Transfer in the genetic background of the susceptible wheat line Thatcher. TcLr9 and TA5605…

Henn, B. M. et al. Genomic ancestry of North Africans supports back-to-Africa migrations. PLOS Genet. 8, e1002397 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Arauna, L. R. et al. Recent historical migrations have shaped the gene pool of Arabs and Berbers in North Africa. Mol. Biol. Evol. 34, 318–329…

Wastewater sample collection, RNA extraction, and sequencing Houston Water collected and provided weekly 24-hour time-weighted composite influent (raw wastewater) samples from 39 wastewater treatment plants (WWTPs) in Houston covering a service area of approximately 580 miles2 and serving over 2.3 million people. In total, 2637 samples were analyzed. Untreated wastewater…

2 hours ago Doozy • 0 Hi guys, I am new to the GERP++, while I found that mendel.stanford.edu/SidowLab/downloads/gerp/ is not avaliable. Though I installed the GERP suit by conda and tried to guess how it works in bitbucket.org/bucklerlab/msa_pipeline/src/master/ (confused with the header of the output GERP_ExpSubst and GERP_RejSubstScore), I…

I would like to generate a logo for the amino acid domain surrounding a particular mutation of interest. I am using the “msa” package in R to generate the multiple sequence alignment based on the full peptide sequence, then I would like to extract a short subset of the consensus…

R is a very flexible programming language, and it allows developers to create their own data structures (called classes) for their packages. Over the years, some packages have become so popular that the classes they use to store data are now used the “standard” representations for particular types of data….

We reasoned that an ideal screening system for functional mRNA delivery would be model independent so that it could be applied in any preclinical model of disease, would consist of multiple measures of protein production that are each orthogonal to any others such that multiple formulations could be tested within…

Liang Y, Lin H, Zou L, Deng X, Tang S. Biosens Bioelectron. 2022;205:114098. Article  CAS  PubMed  PubMed Central  Google Scholar  Telenti A, Hodcroft EB, Robertson DL. Cold Spring Harb Perspect Med. 2022;12:a041390. Article  CAS  PubMed  Google Scholar  Shrestha LB, Foster C, Rawlinson W, Tedla N, Bull RA. Reviews in Medical…

Hi everyone, Hopefully we have some experienced mmseqs users here who can help me with an issue in regards to cascaded clustering. I am a fairly new user of mmseqs and have run into some unexpected behavior which I am unable to resolve. I am attempting to cluster a database…

Acquiring amino acid substitutions via language model consensus We select amino acid substitutions recommended by a consensus of language models. We take as input a single wild-type sequence x = (x1,…,xN)∈ \(\mathcal{X}\)N, where \(\mathcal{X}\) is the set of amino acids, and N is the sequence length. We also require a set of…

By Chris Edwards Communications of the ACM, May 2023, Vol. 66 No. 5, Pages 10-1210.1145/3586582Comments Credit: Veronica Falconieri Hays Two years ago, as the COVID-19 pandemic swept across the world, researchers at DeepMind, the artificial intelligence (AI) and research laboratory subsidiary of Alphabet Inc., demonstrated how it could use machine…

State-of-the-art phylogenomic pipelines require many steps, which can be both time consuming and error prone (Fig. 1a). With Read2Tree, we directly process raw sequencing reads and reconstruct sequence alignments for conventional tree inference methods (Fig. 1b and Supplementary Fig. 1). We start by aligning raw reads to nucleotide sequences derived…

Reconstruction of gene and macro-synteny trees for the three studied Papaver species Syntenic blocks within the three Papaver species were identified with OrthoFinder v2.3.15. Orthologous and paralogous relationships, as well as orthogroups, were inferred using the parameters “-M msa -T fasttree” based on proteome sequences from multiple species. The resulting…

The Michael J. Fox Foundation for Parkinson’s Research (MJFF) has announced what it says is the ‘most significant breakthrough yet’ in the search for a Parkinson’s biomarker: a biological test for Parkinson’s disease. The test demonstrates high diagnostic accuracy, differentiates molecular subtypes and detects disease in individuals before cardinal movement…

Finding a truly effective treatment for Parkinson’s disease – that goes beyond simply managing symptoms – has long been a challenging task and, to this day, there are no available therapeutic options that can effectively slow or stop the underlying disease. However, research and trials to find treatments are ongoing…

Plasmid construction The PVCpnf structural and accessory region (pvc1-16) and payload and regulatory region (Pdp1, Pnf and regulatory genes PAU_RS16570-RS24015) were synthesized de novo (GenScript) and cloned into pAWP78 and pBR322 backbones, respectively. All manipulations involving payload and regulatory plasmids (pPayload) involved standard PCR amplification with Phusion Flash 2x Master…

Is there a function to get the number of aligned sites between pairs of sequences in a multiple sequence alignment in R? 0 Hi, I am working on multiple sequence alignments and I want to obtain the number of aligned sites between each pair of aligned sequences (in other words,…

MSA is a parameter-free error correction method whose performance is determined by the sequence copies used (or sequencing depth). We encode (00-A, 01-T, 10-G, 11-C) a text file named “The Grandmother” into 140 DNA sequences of 120 bases (8 bases for index and 112 bases for data). The error rate…

Assigning prehistoric objects to specific individuals is usually impossible outside of burial contexts. Here we present a non-destructive method for gradually releasing DNA from ancient bone and tooth artifacts. Application of the method to an Upper Paleolithic deer tooth pendant from Denisova Cave (Russia) resulted in the recovery of DNA…

Dear, I recently tried to run strainphlan3 on shallow shotgun sequencing data of 166 skin samples (sequencing depth 12M reads). In the example, underneath, I show the phylogenetic tree of the most abundant species Cutibacterium acnes within all my samples.My first question is, can you use strainphlan3 on shallow shotgun…

PAthreader overview The pipeline of PAthreader is illustrated in Fig. 1, and the details are presented in the Methods section. First, multi-peak distance profiles are obtained by our in-house DeepMDisPre, which may predict multiple possible distances for flexible protein regions. Structure profiles are extracted from PAcluster80, a master structure database built…

Genome reduction is associated with a termite comb-associated lifestyle For our studies, we collected fungus comb samples originating from mounds of Macrotermes natalensis, Odontotermes spp., and Microtermes spp. termites and were able to obtain seven viable Pseudoxylaria cultures (X802 [Microtermes sp.], Mn132, Mn153, X187, X3-2 [Macrotermes natalensis], and X167, X170LB [Odontotermes…

UniProt id to MSA 0 I have UniProt ids of 4000 prokaryotic proteins. I have to do multiple sequence alignments of those proteins. Would anyone suggest to me how to do that? MSA • 28 views • link updated 48 minutes ago by GenoMax 126k • written 2 hours ago…

The formal question I’ve been given is what aligner would I use? There is an issue between forming a data pipeline for ape and the latest and greatest. Its trade and the compromise would be msaClustalOmega(), but the rationale is complicated. I strictly use muscle5 or specifically muscle -super5 option…

doi: 10.1002/bip.23530. Online ahead of print. Affiliations Expand Affiliation 1 Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK. Item in Clipboard Theodoros K Karamanos. Biopolymers. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1002/bip.23530. Online ahead of print. Affiliation 1 Department of Life…

Introduction Cancer is a large group of diseases that have the same basic properties that are caused by cell division or uncontrolled cell proliferation. This irregular process of division produces a mass of cells in an organ or tissue, which leads to the formation of tumours.1,2 Cancer became one of…

Multiple sequence alignment of mtDNA HV1-3 in R 0 Hi all, I would like to perform a multiple sequence alignment from a fasta file containing multiple mitogenomes (mitochondrial genomes). The problem is that some of them are complete linear sequences (mtDNA is circular), but others contain only hypervariable regions 1,…

Introduction Proteases regulate various biological processes including protein synthesis and maturation, activity modification, degradation and turnover. Depending on their catalytic mechanisms, these proteases are primarily classified into cysteine, metallo-, serine, threonine and aspartic protease family (Beers et al., 2004). The latter protease family is known as acid protease family because they…

Chloroplast genome phylogenetic analysis 0 Hello Biostars, Can anybody help me to know whether I have to correct the direction (reverse complement) the Short Single Copy (SSC) region of the Chloroplast genome when I am doing Multiple Sequence Alignment (MSA) for the Phylogenetic inference? I have been trying to learn…

Faking hh-suite workflow / alignment output 1 Given the following: query.fasta -> single entry reference.fasta -> multiple entries I now want to ‘fake’ (or just be able to get) an output that looks like a proper *.hhr alignment file, i.e. as if I aligned the query.fasta against the profiles of…

Chala, B. & Hamde, F. Emerging and re-emerging vector-borne infectious diseases and the challenges for control: A review. Front. Public Health doi.org/10.3389/fpubh.2021.715759 (2021). Article  Google Scholar  Jongejan, F. & Uilenberg, G. The global importance of ticks. Parasitology 129, S3–S14 (2004). Google Scholar  Hornok, S., Kováts, D., Horváth, G., Kontschán, J….

Viral strains utilized in this work The following viral strains have been used in this study: Pandoravirus neocaledonia3, Pandoravirus macleodensis3, Pandoravirus kuranda (this study, ON887157), Mollivirus kamchatka26, Pithovirus sibericum27 and Mimivirus reunion28. Cloning of DNA constructs All primers used in this study are listed in Table S1. All vectors used in…

After a brief 2.5-month hold, Inhibikase Therapeutics’ Parkinson’s disease therapy is heading back to the clinic. The FDA unexpectedly placed a clinical hold on the midstage therapy IkT-148009 in November 2022, sending Inhibikase’s shares tumbling. The phase 2a trial is now set to get back on track, according to a…

I have the peptide sequences and fasta files separately. I first aligned the fasta files using msa package. After that I’m trying to highlight the peptide sequences in the multiple sequence alignment output. I couldn’t find a way to do that. Any suggestions on how to do this would be…

How to convert VCF (with possible predicted gene effects) to protein fasta/MSA 1 How to convert VCF (with possible predicted gene effects) and multiple samples to protein fasta/MSA Input: VCF (possibly with already gene/protein effects predicted via e.g. SnpEff) GFF3 (for the reference protein sequence and maybe to predict effects)…

Loading multiple sequence alignment fasta file for ggmsa 0 Hello, I am trying to use ggmsa to visualize my amino acid multiple sequence alignment (MSA) but the ggmsa() function doesn’t recognize my MSA. Any thoughts how I can correct this? I have been loading my MSA with the following… align…

The purpose of a vaccine (MEBPVC in the current context) is to elicit a strong response from the host immune system against a disease (COVID-19) releasing various neutralizing antibodies which continue to stay in the body to protect the host from any repeat infection thenceforth. Toll-like receptors (TLRs) are the…

AlphaFold: The making of a scientific breakthrough The inside story of the DeepMind team of scientists and engineers who created AlphaFold, an AI system that is recognised as a solution to “protein folding”, a grand scientific challenge for more than 50…

1 SCV000301220.2 Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Pathogenic reviewed by expert panel curation Breast-ovarian cancer, familial, susceptibility to, 2 (unknown ) germline Variant allele predicted to encode a truncated non-functional protein. 1 SCV000785901.2 Counsyl Pathogenic criteria provided,single submitter clinical testing Breast-ovarian cancer, familial, susceptibility to,…

Bio::AlignIO::fasta(3) fasta MSA Sequence input/output stream SYNOPSIS Do not use this module directly. Use it via the Bio::AlignIO class. DESCRIPTION This object can transform Bio::SimpleAlign objects to and from fasta flat files. This is for the fasta alignment format, not for the FastA sequence analysis program. To process the alignments…

Benchmark dataset The following datasets, HomFam and OXFam were used as benchamrk datasets in “Application of the MAFFT sequence alignment program to large data – reexamination of the usefulness of chained guide trees”. HomFam This HomFam dataset is modified version of original HomFam dataset constructed by the authors of Clustal…

ClustalW2 is a general purpose DNA or protein multiple sequence alignment program for three or more sequences. For the alignment of two sequences please instead use our pairwise sequence alignment tools. How does protein alignment work? In typical usage, protein alignments use a substitution matrix to assign scores to amino-acid…

Clustalo failing to complete multiple sequence alignments 0 Hi, I have been using clustalo in the terminal to create multiple sequence alignments for the past few weeks, but every time I try lately it fails. I’ve tried on two computers, with different files. I’ve tried looking up the errors but…

Benchmarking contact prediction First, we benchmarked the long-range contact prediction performance of A-Prot using the FM and FM/TBM targets of CASP13 [24]. The benchmark results show that the performance of our model outperforms that of the existing methods (Table 1). We compared the precision of our model’s top L/5, L/2,…

DeepMind’s AlphaFold 2 grabbed headlines last year by leveraging a transformer-based model architecture to achieve atomic accuracy in protein structure prediction. While the development of deep neural networks (DNNs) has enabled significant performance improvements across a variety of natural language processing and computer vision tasks, AlphaFold’s success showed that DNNs…

Change Residue Output Length in trimAl? 0 Hello, I am looking for a way to change the length of the residues printed in the output of trimAl. Using clustalo, I have generated .aln data that looks like so: chr1_38402816-38409352 ———————————————————————————agatcatgaacttttgctc–ca—agaactattgcaggaa-cataccagga-aagccgagagaatccacagaccctttgaaggaagtggatt chr1_41176265-41182362 ——————————————————————————————————————————————————————————- chr1_42059276-42065372 ——————————————————————————————————————————————————————————- I was able to see 175…

M. Madan Babus Group and the Center for Data-Driven Discovery in the Department of Structural Biology is seeking a highly driven, Full time Machine Learning Research Scientist support the Kalodimos and Babu Groups on the Blue Sky Initiative “Seeing the Invisible in Protein Kinases.” This project is supported by $35…

I am trying to replicate MEGA (models/find best DNA protein models) using R. After reading R AICs and BIC documentation I can’t understand how I can implement it. How can I implement AICs and BICs without having to especify the number of sequences in the fasta file (in case that…

I’ve tried using the standard alphafold2 setup via docker (converted to a singularity container) via the setup described at github.com/kalininalab/alphafold_non_docker, and both result in the following error: […] E1210 12:01:01.009660 22603932526400 hhblits.py:141] – 11:49:18.512 INFO: Iteration 1 E1210 12:01:01.009703 22603932526400 hhblits.py:141] – 11:49:19.070 INFO: Prefiltering database E1210 12:01:01.009746 22603932526400 hhblits.py:141]…

Hey All, I am trying to infer a phylogeny from a multiple sequence alignment using FastTree program, however the program is giving me an error when I run it over the multiple sequence alignment and I can not figure out what the error is saying (not really that informative). My…

Hello folks, I am seeking an advice on Multiple Sequence Alignment that I am trying to get. The fasta file i am trying to align belongs to Sars-Cov-2 Spike protein, it has nearly 600k sequences and ranges from 1270-1275 aa. I have aligned with clustalo and mafft with default parameters….

The program handily beat all competitors, in what one . This will allow us to run alphafold only using CPU ( which is what our VM has). From the developers’ original publication: “The provided inference . The AlphaFold method. Found insideThis book constitutes the refereed proceedings of the First International…

AlphaFold This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document. Any publication that discloses findings arising from…

for the third time worked! Found inside – Page iiThe eight-volume set comprising LNCS volumes 9905-9912 constitutes the refereed proceedings of the 14th European Conference on Computer Vision, ECCV 2016, held in Amsterdam, The Netherlands, in October 2016. Please make sure you have a large enough hard drive space, bandwidth…

In: StatPearls [Internet]. team at our virtual booth on the exhibitor tab. Published online 22 07; DOI: 10.1038/s41586-021-03819-2. Extended Data Fig. Found insideAn important feature of this work is the S-plus subroutines provided for analyzing actual data sets. Coupled with the discussion of new theoretical research, the book should benefit…

Difficulty installing Bioperl for use with GUIDANCE 0 Hi, I am trying to use the Guidance software to analyze a set of 427 sequences. I have the software downloaded and installed the modules indicated in the Guidance user guide (Perl/BioPerl/Ruby), but when I attempt to run Guidance with the following…

Category 3.4 other modification Product putative 6-methylsalicylyltransferase Product (GenBank) ketoacyl-ACP synthase Gene pctTptmR Gene (GenBank) pctT EC number Keyword Note Note (GenBank) Reference ACC A8R0K3 PmId [17827660] Cloning of the pactamycin biosynthetic gene cluster and characterization of a crucial glycosyltransferase prior to a unique cyclopentane ring formation. (J Antibiot (Tokyo)….

Add your e-mail address to receive free newsletters from SCIRP. Select Journal AA AAD AAR AASoci AAST ABB ABC ABCR ACES ACS ACT AD ADR AE AER AHS AID AiM AIT AJAC AJC AJCC AJCM AJIBM AJMB AJOR AJPS ALAMT ALC ALS AM AMI AMPC ANP APD APE APM ARS ARSci AS ASM BLR CC CE CellBio ChnStd CM CMB CN CRCM CS CSTA CUS CWEEE Detection EMAE ENG EPE ETSN FMAR FNS GEP GIS GM Graphene GSC Health IB ICA IIM IJAA IJAMSC IJCCE IJCM IJCNS IJG IJIDS IJIS IJMNTA IJMPCERO IJNM IJOC IJOHNS InfraMatics JACEN JAMP JASMI JBBS JBCPR JBiSE JBM JBNB JBPC JCC JCDSA JCPT JCT JDAIP JDM JEAS JECTC JEMAA JEP JFCMV JFRM JGIS JHEPGC JHRSS JIBTVA JILSA JIS JMF JMGBND JMMCE JMP JPEE JQIS JSBS JSEA JSEMAT JSIP JSS JSSM JST JTR JTST JTTs JWARP LCE MC ME MI MME MNSMS MPS MR MRC MRI MSA MSCE NJGC NM NR NS OALib OALibJ ODEM OJA OJAB OJAcct OJAnes OJAP OJApo OJAppS OJAPr OJAS OJBD OJBIPHY OJBM OJC OJCB OJCD OJCE OJCM OJD OJDer OJDM OJE OJEE OJEM OJEMD OJEpi OJER OJF OJFD OJG OJGas OJGen OJI OJIC OJIM OJINM OJL OJM OJMC OJMetal OJMH OJMI OJMIP OJML OJMM OJMN OJMP OJMS OJMSi OJN OJNeph OJO OJOG OJOGas OJOp OJOph OJOPM OJOTS OJPathology OJPC OJPChem OJPed OJPM OJPP OJPS OJPsych OJRA OJRad OJRD OJRM OJS OJSS OJSST OJST OJSTA OJTR OJTS OJU OJVM OPJ POS PP PST PSYCH SAR SCD SGRE SM SN SNL Soft SS TEL TI UOAJ VP WET WJA WJCD WJCMP WJCS WJET WJM WJNS WJNSE WJNST WJV WSN YM Read more here: Source link

Error while running MEGAX 0 I am running the latest version of MEGA i.e MEGAX. I am trying to run the command megacc but it is throwing an error. My sequences.fas file contains the trimmed multiple sequence alignment (MSA) of 16S rRNA sequences of 1403 organisms in a fasta format….

bcftools merge; retaining sample names 2 When I do bcftools merge, the headers do not retain the filenames.  How can I specify filenames? This is my command  bcftools merge vcf/unfiltered/*.vcf.gz -O z > msa/pooled.vcf.gz However this is the relevant part of my header, despite the filenames I gave it.  Is…

Remove non variable sites from sequence alignment 0 I’m looking for suggestions for programs that will remove nonvariable sites from a fasta/phylip/nexus alignment. I have very large sequence alignments, and I am hoping only to retain variable sites. MSA alignment nexus FASTA sequence • 12 views Login before adding your…

keep getting error with psiblast 1 hello I am trying to calculate the PSSM but I keep getting error , where is the problem in this code ? import os import re def command_pssm(content, output_file,pssm_file): os.system(‘psiblast -in_msa 1ak4.fasta -db allseq.fasta -num_threads 10 -num_iterations 3 -evalue 0.001 -out output_file -out_ascii_pssm PSSM.txt’…

I’m new to both protein structure prediction and the use of AI-based tools like Alphafold2 or RoseTTAFold. And I have a few questions: **1.** Is it possible to use structure prediction by AlphaFold2 to **validate** HMMER based domain sequence predictions? If yes, what would be the steps? I have some…

Filtering MSA by similiarity to a consensus sequence/motif 0 Dear all, anyone knows a good way of filtering or sorting a large multiple sequence alignment (~8000 sequences) by similarity to a given consensus sequence? A solution using python/biopython would be optimal. Any help is appreciated! Best Jonathan biopython motif multiple…

How to visualise a phylogenetic tree with amino acids (double letter repeat) multiple-sequence alignment? 0 I have a fasta file as shown below, rvd.fasta >t1 NI-NG-NR-NN-NG-HD-HD >t_temp5 NG-NG-NI-N*-NR-NI-NN-NG-NG-HD >tal8 NG-NG-NI-N*-ND-NI-NN-NG-NG-H*-NH-NI I have a newick file as follows, tree.newick (tal8:0.49999997,t_temp5:0.47298786,t1:28.37858179); I need to visualise both the tree and rvd.fasta file (multiple-sequence…