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EPSPSClass
Author: Pere Puigbo, PhD
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GPT
Author: Pere Puigbo, PhD
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OPTIMIZER (Lite Version)
Author: Pere Puigbo, PhD
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Puigbo P, Guzman E, Romeu A and Garcia-Vallve S (2007) OPTIMIZER: A web server for optimizing the codon usage of DNA sequences. Nucleic Acids Research 35:W126-W131.
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OPTIMIZER is an on-line PHP application that optimizes the codon usage of a DNA sequence to increase its expression level. Users can introduce their own preference tables to be used in the optimization process or use pre-computed tables from several prokaryotic species under a strong translational selection. Three methods of optimization are available: the 'one amino acid - one codon' approach, a random approach or an intermediate one. Several options, such as avoiding specific restriction sites and several outputs, are also available. This server can be useful for predicting and optimizing the level expression of a gene in heterologous gene expression.
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CAIcal/E-CAI
Author: Pere Puigbo, PhD
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TOPD/fMtS
Author: Pere Puigbo, PhD
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Highly Expressed Genes Database
Author: Pere Puigbo, PhD
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     Simplified Version
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Puigbo P, Romeu A and Garcia-Vallve S. 2008. HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection.Nucleic Acids Research, 36:D524-D527.
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The HEG-DB is a genomic database that includes the prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection. The current version of the database contains general features for almost 200 genomes under translational selection, including the correspondence analysis of the relative synonymous codon usage for all genes, and the analysis of their highly expressed genes. For each genome, the database contains functional and positional information about the predicted group of highly expressed genes. This information can also be accessed using a search engine. Among other statistical parameters, the database also provides the Codon Adaptation Index for all of the genes using the codon usage of the highly expressed genes as a reference set. The "Pathway Tools Omics Viewer" from the BioCyc database enables the metabolic capabilities of each genome to be explored, particularly those related to the group of highly expressed genes.
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Horizontal Gene Tranfer Database
Author: Santiago Garcia-Vallve, PhD
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     Old version
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DendroUPGMA
Author: Santi Garcia-Vallve, PhD
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Garcia-Vallve S, Palau J and Romeu A. (1999) Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis. Molecular Biology and Evolution 9:1125-1134.
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Use this program to create a dendrogram from a set of variables. The program calculates a similarity coefficient between pairs of sets of variables, transforms these coefficients into distances and makes a clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm.
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ORFsearch
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ORFsearch
Author: Pere Puigbo, PhD
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Puigbo P et al. (2006) ORFsearch at URL: http://genomes.urv.cat/ORFsearch
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A web server utility that search Open Reading Frames or translates DNA sequences.
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Translate
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Translate
Author: Santi Garcia-Vallve, PhD
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S. Garcia-Vallve et al. (2002) Translate at URL: http://www.tinet.org/~debb/Translate/
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Use this program to translate a set of DNA sequences and obtain the proteins encoded, the %G+C, the Codon usage, the amino acid composition or the RSCU values.
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LDIST
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Levenshtein distance
Author: Pere Puigbo, PhD
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Minimum number of single-character edits (insertions, deletions or substitutions) to transform one word into the other.
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