• CodonO

  • Referenced in 2 articles [sw17252]
  • informatics method for measuring synonymous codon usage bias within and across genomes. Codon usage bias ... pattern. Previous research showed that the codon usage bias was associated with many biological processes ... specificity. We reviewed major methods of codon usage bias measurement. Since most of the existing ... only suitable for the comparison of codon usage bias within a single genome, we introduced...
  • BCAWT

  • Referenced in 1 article [sw30689]
  • BCAWT: Automated tool for codon usage bias analysis for molecular evolution. There are no tools ... whole automated workflow for codon usage bias analysis. Using python 3.7 BCAW Tool ( Bio Codon ... complete automated workflow to analyze the codon usage bias for genes and genomes...
  • CAIcal

  • Referenced in 1 article [sw37897]
  • first developed to measure the synonymous codon usage bias for a DNA or RNA sequence ... quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon...
  • SSCU

  • Referenced in 1 article [sw25675]
  • calculate the strength of selected codon usage bias (sscu, also named as s_index) based ... focus only on four pairs of codons with universal translational advantages in all bacterial species ... optimal/non-optimal codons. (3) Optimal codon lists (selected codons) can be calculated by either op_highly ... Akashi’s test. (4) The detailed codon usage information, such as RSCU value, number...
  • INCA

  • Referenced in 1 article [sw37894]
  • codon frequencies and several usage indices, such as ‘codon bias’, effective ... visual detection of various trends in codon usage. Finally, INCA includes a specific unsupervised neural...
  • EuGene

  • Referenced in 1 article [sw28666]
  • synonymous codon usage and CAI), codon context (CPS and codon pair bias), GC content, hidden...
  • Matlab

  • Referenced in 13544 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 9969 articles [sw00771]
  • R is a language and environment for statistical...
  • Bioconductor

  • Referenced in 319 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • LIBSVM

  • Referenced in 1185 articles [sw04879]
  • LIBSVM is a library for Support Vector Machines...
  • C4.5

  • Referenced in 1164 articles [sw12176]
  • C4.5: programs for machine learning. (C4.5 has been...
  • KEGG

  • Referenced in 280 articles [sw13866]
  • KEGG: Kyoto Encyclopedia of Genes and Genomes. KEGG...
  • Python

  • Referenced in 2091 articles [sw14460]
  • Python is a widely used high-level, general...
  • PROSITE

  • Referenced in 39 articles [sw17326]
  • PROSITE: a documented database using patterns and profiles...
  • BLAST

  • Referenced in 251 articles [sw17334]
  • Basic Local Alignment Search Tool. BLAST finds regions...
  • iRSpot-TNCPseAAC

  • Referenced in 31 articles [sw22412]
  • iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition...
  • iAMP-2L

  • Referenced in 23 articles [sw22416]
  • iAMP-2L: a two-level multi-label classifier...