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Links tagged with 'codon'

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Codon Usage DatabaseDatabase Content

http://www.kazusa.or.jp/codon/

DNA > Structure and Sequence Feature Detection
Model Organisms > General Resources

Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.

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tagscodon factual databases

CodonOTool Content

http://digbio.missouri.edu/software/index.html

DNA > Structure and Sequence Feature Detection
Model Organisms > General Resources

CodonO is a method for measuring synonymous codon usage bias within and across genomes.

NAR Web Server Issue 2007
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tagsarchaeal dna archaeal genome bacterial dna bacterial genome base composition codon computational biology computer simulation gc rich sequence genetic code genetic models genome species specificity

DyNAVacSTool Content

http://miracle.igib.res.in/dynavac/

DNA > Tools For the Bench
Human Genome > Health and Disease

DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences.

NAR Web Server Issue 2006
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tagscodon computational biology cpg islands dna primers dna vaccines drug design gene expression polymerase chain reaction restriction mapping systems integration

GenDecoderTool Content

http://darwin.uvigo.es/software/gendecoder.html

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Multiple Sequence Alignments

GenDecoder is a prediction server for animal mitochondrial genetic codes. It provides information about codon-usage, amino acid composition, GC content and a final genetic code prediction for a mitochondrial genome sequence.

NAR Web Server Issue 2006
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tagsamino acid sequence animals base sequence codon conserved sequence mitochondrial genes molecular evolution protein biosynthesis sequence alignment sequence analysis

GLUE, GLUE-IT, PEDEL, PEDEL-AA and DRIVeRTool Content

http://guinevere.otago.ac.nz/stats.html

DNA > Tools For the Bench

GLUE, PEDEL, and DRIVeR are tools for estimating completeness and diversity in randomized protein-encoding libraries; useful for guiding library design and for analyzing results. GLUE Including Translation (GLUE-IT) finds the expected amino acid completeness of libraries. PEDEL-AA calculates amino acid statistics for libraries generated by epPCR.

NAR Web Server Issue 2008
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tagsalgorithms chemical models codon computer simulation directed molecular evolution dna dna mutational analysis dna sequence analysis gene library genetic models genetic variation molecular evolution mutagenesis mutation peptide library point mutation polymerase chain reaction protein sequence analysis proteins statistical models

JCatTool Content

http://www.jcat.de/

DNA > Structure and Sequence Feature Detection
Model Organisms > General Resources

JCAT (Java Codon Adaptation Tool) is a tool that can adjust the codon usage of an input sequence to the selected organism. Useful for improving the expression of foreign genes in hosts with different codon usage.

NAR Web Server Issue 2005
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tagsalgorithms animals caenorhabditis elegans codon escherichia coli gene expression pseudomonas aeruginosa recombinant proteins species specificity

MKTTool Content

http://mkt.uab.es

DNA > Sequence Polymorphisms

Standard and Generalized McDonald-Kreitman Test (MKT) is a web tool for the molecular level detection of signatures of natural selection.

NAR Web Server Issue 2008
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tagsanimals codon dna sequence analysis drosophila genetic selection genetic variation

OPTIMIZERTool Content

http://genomes.urv.es/OPTIMIZER/

DNA > Structure and Sequence Feature Detection
Expression > Protein Expression

OPTIMIZER is an application that optimizes the codon usage of a DNA sequence. This server can be used to predict and optimize the level expression of a gene in heterologous gene expression systems.

This content is being maintained by ppuigbo.

NAR Web Server Issue 2007
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tagsalgorithms animals base sequence codon computational biology dna dna sequence analysis gene expression gene expression regulation molecular sequence data protein biosynthesis ribosomes

PAL2NALTool Content

http://coot.embl.de/pal2nal/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Other Alignment Tools

PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated.

NAR Web Server Issue 2006
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tagscodon dna sequence analysis exons protein sequence analysis sequence alignment

RevTransTool Content

http://www.cbs.dtu.dk/services/RevTrans/

Sequence Comparison > Multiple Sequence Alignments

RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment.

NAR Web Server Issue 2003
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tagsamino acid substitution base sequence codon dna sequence analysis mutation protein sequence analysis sequence alignment

RF_DYMHCTool Content

http://www.bioinf.seu.edu.cn/Recombination/rf_dymhc.htm

DNA > Structure and Sequence Feature Detection
Model Organisms > Yeast

RF_DYMHC (Random Forest-Based System for Detecting Yeast Meiotic Recombination Hotspots and Coldspots) predicts recombination hot/cold spots in the yeast genome.

NAR Web Server Issue 2007
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tagsalgorithms artificial intelligence automated pattern recognition chromosome mapping codon computational biology dna sequence analysis fungal genome genetic recombination meiosis nucleotides saccharomyces cerevisiae

RNAfoldTool Content

http://www.tbi.univie.ac.at/cgi-bin/RNAfold.cgi

RNA > Structure Prediction, Visualization, and Design

Predict RNA secondary structure from sequence; note sequence length limit.

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tagsalgorithms alzheimer disease amyloid beta-protein precursor base composition base sequence catalytic rna codon humans molecular sequence data nucleic acid conformation thermodynamics

SelectomeDatabase Content

http://selectome.unil.ch/

Protein > Databases
Protein > Sequence Features
Sequence Comparison > Analysis of Aligned Sequences

Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. The web interface of Selectome enables queries according both to the results of positive selection tests, and to gene related criteria. Test results including positively selected sites can be visualized on the tree, and on the protein sequence alignment.

This content is being maintained by selectome.

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tagsamino acid sequence homology animals codon computational biology computing methodologies gene duplication genes genetic databases genetic selection medical informatics applications phylogeny proteins software design vertebrates