Search Results for "codon"
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Showing 29 open source projects for "codon"
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Codon
A high-performance, zero-overhead, extensible Python compiler
Codon is a high-performance Python compiler that compiles Python code to native machine code without any runtime overhead. Typical speedups over Python are on the order of 100x or more, on a single thread. Codon supports native multithreading which can lead to speedups many times higher still. The Codon framework is fully modular and extensible, allowing for the seamless integration of new modules, compiler optimizations, domain-specific languages and so on. -
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VisualCUF
Visual comparator of codon usage frequencies (CUFs)
VisualCUF visually compares two or three codon usage frequencies. The input files are .cuf files produced by the cufCDS program. -
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cufCDS
Codon usage frequency (CUF) calculator of coding fasta sequences
cufCDS calculates codon usage frequency (CUF) of coding sequences (CDSs). The input of this application is a fasta file of coding sequences. The application removes CDSs that are not divisible by 3 and counts the codons of each CDS after removing the start and stop codons. The result for each CDS is reported in the .gcf file. The following files are also produced: .fss, which reports the frequencies of codons used as start and stop signals .lss, which contains the list of start and stop codons of each gene. .cuf, which reports the total frequencies and the fraction of synonymous codons. -
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MetaEntropy
R package for Virome Mutational Analysis
Estimates Shannon entropy, per gene and per genomic position, associated with non-synonymous mutation frequencies in viral populations, such as wastewater samples. The package uses codon translations for functional insights. Each amino acid can be treated as an individual state, resulting in a 20-state entropy computation, or grouped into one of six physicochemical classes, adding further functional context. Provides normalized values (0-1 scale) to facilitate the direct comparison of different genomic positions or total functional entropy across multiple metagenomes. ... -
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CodonU
A python project for analysis of codon usage for gene or genome analys
With CodonU, you can now easily read, manipulate, and analyze various file formats used in this kind of analysis, and generate high-quality graphics suitable for publishing. This open-source project incorporates various statistical measures necessary for codon usage analysis, including codon adaptation index, codon bias index, Gravy score, and correspondence analysis for both nucleotide and protein sequences. Start using CodonU today and see how it can revolutionize your genomics research! Find more at: https://github.com/SouradiptoC/CodonU Documentation link: https://souradiptoc.github.io/CodonU Example Link: https://github.com/SouradiptoC/CodonU/tree/master/Examples -
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CODON SOFTWARE
The dataset and codon project files are available here.
...Over the years, numerous pipelines and computational tools have been developed aiming to automate this task and assist researchers in gaining knowledge about target genes of study. However, even with these technological advances, manual annotation or manual curation is necessary. To assist with this problem, we present CODON, a tool for the prediction, annotation, and manual curation of genomic data. This software makes use of a finite state machine in the prediction process and automatically annotates products based on information obtained from the Uniprot database. CODON is equipped with a simple and intuitive graphic interface that assists with manual curation, providing the user with decision making abilities throughout the analysis including in identity, length of alignment, and name of the organism in which the product obtained a hit. -
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Microbial Genomics Tools
MGT is Codon usage analysis tool
...Microbial Genomic Tool (MGT 1.0), the first version is developed for In-silico research bacteria genomic study and useful for the Students and research scholars working in the field of Microbial Genomics. 2. User-friendly graphical interface 3. It provides application for calculation of codon frequency, RSCU, AT3, GC3, Nc Enc, nucleotide composition and percent values. 4. Result can be viewed in MS-Excel sheet. 5. MGT development was initiated with the future intention to provide multi-application software for bacterial genome analysis. -
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CUCAA tool
Codon Usage Co-Adaptation Analysis Tool "CUCAA Tool"
Tools are available to analysis the codon usage, but there are no tools available focusing on analyzing the codon usage co-adaptation between viruses and their hosts. Therefore, Codon Usage Co-Adaptation Analysis Tool "CUCAA Tool" were developed by python 3.7. The tool can calculate various codon usage bias measurements as effective number of codons, codon adaptation index, relative codon deoptimization index, similarity index, as well as a simple cluster machine learning approach to see if the viruses will be clustered with the host codon usage or not. -
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BCAW Tool
Bio Codon Analysis Workflow Tool
BCAWT was developed using python 3.7 with build in and third-party modules. The usage of BCAWT is made to be very easy where users have only to input a fasta format file containing genes to be analyzed, and a bunch of analysis will be performed with 23 different output files -
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mfsizes
Multi-FASTA sequence (DNA or protein) statistics calculator.
A simple command-line utility to calculate biological sequence (DNA or protein) sizes in a (multi) FASTA file. It gives averages, GC (or methionine) content, N50, N90, N95, number of N's, and total bases, and can also report by codon if requested. -
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GetX
An automated mutation cassette design tool for scarless genome editing
...GetX allows the user to design synthetic DNA fragments required to perform bacterial genome editing with simple inputs of 1) genome information from the target strain and 2) information for the desired mutation. GetX designs DNA fragments for introduction of sequences for protein tagging, deletions, insertions, and point mutations. It also designs synonymous codon fragments required to manipulate essential target genes to enable survival of the strain during the genome editing procedure. GetX provides genbank and fasta format files for a mutation template plasmid, a mutation cassette, and a sequence around the mutation site to guide the user through the design of the materials required for the scarless bacterial genome editing method. -
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ingap-cdg
codon-based de Bruijn graph algorithm for gene construction
...Here we present a novel algorithm, inGAP-CDG, for effective construction of full-length and non-redundant CDSs from unassembled transcriptomes. inGAP-CDG achieves this by combining a newly developed codon-based de bruijn graph to simplify the assembly process and a machine learning based approach to filter false positives. Compared with other methods, inGAP-CDG exhibits significantly increased predicted CDS length and robustness to sequencing errors and varied read length. -
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DaMold
a data mining platform for variant annotation and visualization.
...It is easy-to-use software, which provides flexible input options and accepts variants in VCF and BED formats. For each variant DaMold predicts the variant effect, such as codon change, and amino acid change. Furthermore, it cross-links each variant with more than 30 clinically relevant public databases, which contain already reported SNPs and INDELs from previous experimental studies along with associated genomic, proteomic, and clinical information. DaMold seamlessly integrates six widely used genome browser such as the UCSC genome browser, Ensembl genome browser, GWAS central genome browser, HapMap genome browser, 1000 Genomes browser, and NCBI variation viewer. ... -
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REDO
REDO - RNA Editing Detection in Organelle
REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in... -
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riboshape
Predicting ribosome footprint profile shapes from transcript sequences
Riboshape is a suite of algorithms to predict ribosome footprint profile shapes from transcript sequences. It applies kernel smoothing to codon sequences to build predictive features, and uses these features to builds a sparse regression model to predict the ribosome footprint profile shapes. Reference: Liu, T.-Y. and Song, Y.S. Prediction of ribosome footprint profile shapes from transcript sequences. Proceedings of ISMB 2016, Bioinformatics, Vol. 32 No. 12 (2016) i183-i191. -
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CEMAsuite
Consensus/Degenerate Primer Design Application
CEMAsuite, is an interactive Java-based application with the ability to (i) construct a codon-equivalent multiple alignment (CEMA) from a protein multiple sequence alignment (MSA) file, (ii) generate and score each position in the consensus DNA sequence using multiple algorithms, (iii) design single-degeneracy primer backbones using Primer3 (Untergasser et al. 2012), (iv) estimate the stability of degenerate primers on each of the coding sequences within the CEMA, and (v) export intermediate results in various formats. ... -
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MNV Annotation Corrector
Multi-nucleotide Variation Annotation Corrector for NGS SNV callers
...These complex mutations consist of two or more consecutive nucleotide substitutions, but can only be detected in the format of several single nucleotide variations (SNV) by most variant callers and annotated separately, which likely leads to incorrect amino acid prediction when more than one mutated bases occur within the same protein codon. MAC screens through a list of user-provided SNVs and the matching BAM file to accurately identify MNV, and use existing annotators (currently supports ANNOVAR/SnpEff/VEP) to provide corrected amino acid prediction. -
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codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction. Given a set of species characterized by their DNA sequences as input, codonPhyML will return the phylogenetic tree that best describes their evolutionary relationship. Our paper describing codonPhyML has been published in the journal "Molecular Biology and Evolution" (MBE). For more details, follow the link: http://mbe.oxfordjournals.org/content/30/6/1270. codonPhyML is on the cover of MBE!
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lccs
Longest Common Coding Subsequence algorithm
This is an implementation, in C++, of the Longest Common CDS Subsequence algorithm. Given two CDS (coding) sequences A and B, program will find the longest sequence of CDS that is common and ordered in A-B and B-A. -
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ViVaMBC
Model-based clustering to estimate viral diversity from Illumina.
ViVaMBC is the first method to call viral variants directly at codon level and where the potential of second best base calls is explored. -
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VIGOR3
Annotation of Viral Genomes
VIGOR is a tool for annotating coding genes in viral genomes. It was developed by Jeffrey Hoover and Shiliang Wang for The JCVI Genomic Sequencing Center for Infectious Diseases (GSCID). http://www.biomedcentral.com/content/pdf/1471-2105-11-451.pdf contact: Jeff Hoover 301-540-7858 jefhv@aol.com -
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Correct-O-Chem
Converts chemical formulae into their correct notation.
...New to Version 2.11: -(Remember to run Correct-O-Chem as admin - Right-click on the "Correct-O-Chem" executable and select Properties, Compatibility and tick Run as administrator) -Updated "Help" menu -Codon Calculator -Provides an input box (in any window) that enables you to enter either a codon or amino acid (name, 3 letter identifier or 1 letter identifier - NO SPACES) and displays the corresponding amino acid/codons. ctrl+` (the button to the left of the "1" - not apostrophe) or right-clicking on the tool tray icon and selecting Codon Calculator will activate the pop-up box... -
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CUO
Codon Usage Optimizer
CUO is a GUI-based multiplatform software written in Java. It is open source and built with a user/developer-friendly structure. The main function of the software at the current development stage is to optimize genes to be transformed into the Chlamydomonas reinhardtii chloroplast genome although it can be used to optimize genes into other hosts as well. The main tool in CUO, Moptimizer, introduces a semi-automatic way of gene optimization which provides more flexibility and accuracy during... -
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Simulation of nucleotide and codon sequences from populations with recombination, migration and growth rates. https://github.com/MiguelArenas/recodon
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This application transcribes basic codons and tells you the amino acid it codes for, the tRNA anti-Codon, and give you a 3D structural model of the amino acid and 2D picture of its chemical structure. Analysis reports can then be printed by the user.
