Tag: msa

VCV000038126.28 Observations – ClinVar – NCBI

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,…

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fasta MSA Sequence input/output stream

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…

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MAFFT benchmark

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…

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What is ClustalW alignment?

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…

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Clustalo failing to complete multiple sequence alignments

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…

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A-Prot: protein structure modeling using MSA transformer | BMC Bioinformatics

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,…

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HPC-AI’s FastFold Shortens AlphaFold Training Time from 11 Days to 67 Hours

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…

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Change Residue Output Length in trimAl?

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…

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Bioinformatics Research Scientist (Blue Sky Initiative), Memphis, Tennessee

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…

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r – Displaying BIC and AICs from MSA nucleotide multisequence fasta file

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…

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alphafold2: HHblits failed – githubmemory

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]…

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FastTree error while constructing tree

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…

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Aligning large sets of sequences

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….

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deepmind alphafold github

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…

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Install alphafold on the local machine, get out of docker.

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…

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alphafold colab github

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…

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highly accurate protein structure prediction with alphafold

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…

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Difficulty installing Bioperl for use with GUIDANCE

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…

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Pact_00210 : CDS information — DoBISCUIT

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)….

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SCIRP Open Access

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

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Error while running MEGAX

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….

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bcftools merge; retaining sample names

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…

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Remove non variable sites from sequence alignment

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…

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keep getting error with psiblast

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’…

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alphafold online availability and use case

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…

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Filtering MSA by similiarity to a consensus sequence/motif

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…

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How to visualise a phylogenetic tree with amino acids (double letter repeat) multiple-sequence alignment?

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…

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