Browsing by Author "Melo Ledermann, Francisco Javier"

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    A composite score for predicting errors in protein structure models
    (2006) Eramian, D.; Shen, M. Y.; Devos D.; Melo Ledermann, Francisco Javier; Sali, A.; Marti Renom, M. A.
    Reliable prediction of model accuracy is an important unsolved problem in protein structure modeling. To address this problem, we studied 24 individual assessment scores, including physics-based energy functions, statistical potentials, and machine learning–based scoring functions. Individual scores were also used to construct ∼85,000 composite scoring functions using support vector machine (SVM) regression. The scores were tested for their abilities to identify the most native-like models from a set of 6000 comparative models of 20 representative protein structures. Each of the 20 targets was modeled using a template of <30% sequence identity, corresponding to challenging comparative modeling cases. The best SVM score outperformed all individual scores by decreasing the average RMSD difference between the model identified as the best of the set and the model with the lowest RMSD (ΔRMSD) from 0.63 Å to 0.45 Å, while having a higher Pearson correlation coefficient to RMSD (r = 0.87) than any other tested score. The most accurate score is based on a combination of the DOPE non-hydrogen atom statistical potential; surface, contact, and combined statistical potentials from MODPIPE; and two PSIPRED/DSSP scores. It was implemented in the SVMod program, which can now be applied to select the final model in various modeling problems, including fold assignment, target–template alignment, and loop modeling.
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    A Composite Score for Predicting Errors in Protein Structure Models
    (2006) Eramian, D.; Melo Ledermann, Francisco Javier
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    A new multiplex PCR assay for the simultaneous detection of vancomycin-resistant enterococci from rectal swabs
    (2010) Benadof, D.; San Martín, M.; Aguirre, J.; Paredes, L.; Malig, R.; Melo Ledermann, Francisco Javier; Lehouque, G.
    Objectives This study describes the diagnostic performance of a recently available multiplex PCR-based kit for the simultaneous detection and identification of Enterococcus faecium, Enterococcus faecalis, vanA, vanB, vanC1 and vanC2/C3 genes, directly from rectal swabs constituting the most complete existing molecular assay currently available. Methods The diagnostic performance of this assay was evaluated by a multicenter study involving three independent public hospitals and consisted in the analysis of 187 rectal swabs from patients at high risk for vancomycin-resistant enterococci colonization. Results When bacteria culture was used as the gold standard, the sensitivity, specificity, positive and negative predicted values for the assay were 96.8%, 76.0%, 67.7% and 97.9%, respectively. When a composite reference standard consisting of culture and DNA sequencing of PCR products was used as the gold standard, the sensitivity, specificity, positive and negative predicted values for the PCR-based assay were 97.8%, 96.9%, 96.7% and 97.9%, respectively. Conclusions Based on these results, we conclude that this assay is considerably more sensitive than traditional microbiological methods for detecting vancomycin-resistant enterococci from rectal swabs. It is also much faster than culture. We believe that the implementation of this assay in routine clinical laboratories could help to reduce hospital-acquired vancomycin-resistant enterococci infections.
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    A novel extracellular multicopper oxidase from Phanerochaete chrysosporium with ferroxidase activity
    (2003) Larrondo Castro, Luis Fernando; Salas, L.; Melo Ledermann, Francisco Javier; Vicuña, Rafael; Cullen, D.
    Lignin degradation by the white rot basidiomycete Phanerochaete chrysosporium involves various extracellular oxidative enzymes, including lignin peroxidase, manganese peroxidase, and a peroxide-generating enzyme, glyoxal oxidase. Recent studies have suggested that laccases also may be produced by this fungus, but these conclusions have been controversial. We identified four sequences related to laccases and ferroxidases (Fet3) in a search of the publicly available P. chrysosporium database. One gene, designated mco1, has a typical eukaryotic secretion signal and is transcribed in defined media and in colonized wood. Structural analysis and multiple alignments identified residues common to laccase and Fet3 sequences. A recombinant MCO1 (rMCO1) protein expressed in Aspergillus nidulans had a molecular mass of 78 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and the copper I-type center was confirmed by the UV-visible spectrum. rMCO1 oxidized various compounds, including 2,2′-azino(bis-3-ethylbenzthiazoline-6-sulfonate) (ABTS) and aromatic amines, although phenolic compounds were poor substrates. The best substrate was Fe2+, with a Km close to 2 μM. Collectively, these results suggest that the P. chrysosporium genome does not encode a typical laccase but rather encodes a unique extracellular multicopper oxidase with strong ferroxidase activity.
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    A Tool to Assist the Study of Specific Features At Protein Binding Sites
    (2003) Santander, V.; Melo Ledermann, Francisco Javier
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    A tool to assist the study of specific features at protein binding sites
    (2003) Santander, V.; Portales, M. A.; Melo Ledermann, Francisco Javier
    The Protein Data Bank contains a large amount of proteins that have been solved with small ligands bound to them. This constitutes a rich source of information for the study of the specific requirements of protein sites to bind small molecules with a favorable free energy. The specific atomic composition and three-dimensional geometric restraints of protein binding sites for different ligands could be easily obtained from there. The development of accurate binding site descriptors in proteins constitutes a valuable tool to assist in the large-scale prediction and annotation of protein function in whole genomes. In this work, an integrated database containing some processed and calculated protein/ligand information is described. It is expected that this database will constitute a useful tool for people working in the prediction of protein function from its structure. The database is accessible from the Internet through a web server located at: http://protein.bio.puc.cl
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    Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets
    (2006) Melo Ledermann, Francisco Javier; Marti Renom, M. A.
    Reduced or simplified amino acid alphabets group the 20 naturally occurring amino acids into a smaller number of representative protein residues. To date, several reduced amino acid alphabets have been proposed, which have been derived and optimized by a variety of methods. The resulting reduced amino acid alphabets have been applied to pattern recognition, generation of consensus sequences from multiple alignments, protein folding, and protein structure prediction. In this work, amino acid substitution matrices and statistical potentials were derived based on several reduced amino acid alphabets and their performance assessed in a large benchmark for the tasks of sequence alignment and fold assessment of protein structure models, using as a reference frame the standard alphabet of 20 amino acids. The results showed that a large reduction in the total number of residue types does not necessarily translate into a significant loss of discriminative power for sequence alignment and fold assessment. Therefore, some definitions of a few residue types are able to encode most of the relevant sequence/structure information that is present in the 20 standard amino acids. Based on these results, we suggest that the use of reduced amino acid alphabets may allow to increasing the accuracy of current substitution matrices and statistical potentials for the prediction of protein structure of remote homologs.
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    Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression
    (2006) Malig, R.; Varela, C.; Agosin T., Eduardo; Melo Ledermann, Francisco Javier
    Background In this study, we present a robust and reliable computational method for tag-to-gene assignment in serial analysis of gene expression (SAGE). The method relies on current genome information and annotation, incorporation of several new features, and key improvements over alternative methods, all of which are important to determine gene expression levels more accurately. The method provides a complete annotation of potential virtual SAGE tags within a genome, along with an estimation of their confidence for experimental observation that ranks tags that present multiple matches in the genome. Results We applied this method to the Saccharomyces cerevisiae genome, producing the most thorough and accurate annotation of potential virtual SAGE tags that is available today for this organism. The usefulness of this method is exemplified by the significant reduction of ambiguous cases in existing experimental SAGE data. In addition, we report new insights from the analysis of existing SAGE data. First, we found that experimental SAGE tags mapping onto introns, intron-exon boundaries, and non-coding RNA elements are observed in all available SAGE data. Second, a significant fraction of experimental SAGE tags was found to map onto genomic regions currently annotated as intergenic. Third, a significant number of existing experimental SAGE tags for yeast has been derived from truncated cDNAs, which are synthesized through oligo-d(T) priming to internal poly-(A) regions during reverse transcription. Conclusion We conclude that an accurate and unambiguous tag mapping process is essential to increase the quality and the amount of information that can be extracted from SAGE experiments. This is supported by the results obtained here and also by the large impact that the erroneous interpretation of these data could have on downstream applications.
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    Adaptive evolution of the insulin gene in caviomorph rodents
    (2005) Opazo, J. C.; Palma Vásquez, Ramón Eduardo; Melo Ledermann, Francisco Javier; Lessa, E. P.
    Insulin is a conservative molecule among mammals, maintaining both its structure and function. Rodents that belong to the Suborder Hystricognathi represent an exception, having a very divergent molecule with unusual physiological properties. In this work, we analyzed the evolutionary pattern of the insulin gene in caviomorph rodents (South American hystricomorph rodents). We found that these rodents have higher rates of nonsynonymous:synonymous substitutions (dN/dS) than nonhystricomorph rodents and that values are heterogeneous inside the group. We estimated codons under positive selection, specifically the second binding site (A13 and B17) and others related with hexamerization (B18, B20, and B22). In the monomer structure, all selected sites formed a single patch around the second binding site. In the hexamer structure, these amino acids were grouped into three major patches. In this structure, contacts between B chains involved all selected sites (except B18), and between faces in the center of the molecule, all contacts were among selected sites. While there is no clear hypothesis regarding the cause of this drastic change, experimental evidence does show that this group of rodents has some peculiarities in growth function, and, whether coincidental or not, these changes appeared together with important changes in life-history traits.
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    All-atom knowledge-based potential for RNA structure prediction and assessment
    (2011) Capriotti, E.; Norambuena, T.; Marti Renom, M. A.; Melo Ledermann, Francisco Javier
    Motivation: Over the recent years, the vision that RNA simply serves as information transfer molecule has dramatically changed. The study of the sequence/structure/function relationships in RNA is becoming more important. As a direct consequence, the total number of experimentally solved RNA structures has dramatically increased and new computer tools for predicting RNA structure from sequence are rapidly emerging. Therefore, new and accurate methods for assessing the accuracy of RNA structure models are clearly needed. Results: Here, we introduce an all-atom knowledge-based potential for the assessment of RNA three-dimensional (3D) structures. We have benchmarked our new potential, called Ribonucleic Acids Statistical Potential (RASP), with two different decoy datasets composed of near-native RNA structures. In one of the benchmark sets, RASP was able to rank the closest model to the X-ray structure as the best and within the top 10 models for ∼93 and ∼95% of decoys, respectively. The average correlation coefficient between model accuracy, calculated as the root mean square deviation and global distance test-total score (GDT-TS) measures of C3′ atoms, and the RASP score was 0.85 and 0.89, respectively. Based on a recently released benchmark dataset that contains hundreds of 3D models for 32 RNA motifs with non-canonical base pairs, RASP scoring function compared favorably to ROSETTA FARFAR force field in the selection of accurate models. Finally, using the self-splicing group I intron and the stem-loop IIIc from hepatitis C virus internal ribosome entry site as test cases, we show that RASP is able to discriminate between known structure-destabilizing mutations and compensatory mutations. Availability: RASP can be readily applied to assess all-atom or coarse-grained RNA structures and thus should be of interest to both developers and end-users of RNA structure prediction methods. The computer software and knowledge-based potentials are freely available at http://melolab.org/supmat.html.
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    Análisis in vitro de los diferentes modos de unión a ADN de los factores de transcripción MarA y Rob
    (2021) Geoffroy Jarpa, Consuelo Ignacia; Melo Ledermann, Francisco Javier; Pontificia Universidad Católica de Chile. Facultad de Ciencias Biológicas
    El proceso de reconocimiento molecular entre proteínas y ADN es fundamental para la vida. MarA y Rob son 2 factores de transcripción de Escherichia coli pertenecientes a la familia AraC/XylS, cuyos miembros presentan una alta similitud de secuencia y se encuentran relacionados a la regulación de genes involucrados en resistencia a antibióticos, tolerancia estrés oxidativo y resistencia a disolventes orgánicos y metales pesados [1]. La estructura de ambas proteínas incluye un dominio de reconocimiento a ADN organizado en un motivo HTH bipartito, con dos hélices clave en el reconocimiento de secuencias (Hélices 3 y 6). Adicionalmente Rob presenta un dominio regulatorio en el extremo C-terminal, cuya función aún no es bien conocida. Estudios cristalográficos previos, sugieren que ambos factores de transcripción reconocen y se unen a sus secuencias promotoras de forma distinta. Mientras que MarA interactúa con dos secuencias nucleotídicas clave denominadas cajas A y B de la región promotora y une ambas hélices al surco mayor del ADN deformándolo, Rob reconoce ambas cajas, pero tan solo se une a una de ellas sin alterar la estructura nucleica. En este estudio se abordan diferentes interrogantes y se combinan e integran datos experimentales, estadísticos y computacionales lo que permite comprender los mecanismos de reconocimiento y las diferencias planteadas. El factor de transcripción purificado se agregó in vitro a los distintos promotores degenerados y las secuencias unidas y no unidas se separaron. La estrategia general fue crear una biblioteca de sitios de unión potenciales, a partir de las secuencias unidas. Ambos extremos de las secuencias de la biblioteca tienen sitios de unión de partidores de modo que pudieron amplificarse mediante PCR y ser secuenciados mediante secuenciación masiva. Por otro lado los promotores degenerados abarcaron tanto el promotor mar como el promotor micF completo y se fueron cubriendo regiones de 4 nucleótidos. Esto permitió tener una mirada global de los factores que juegan un rol importante en el reconocimiento específico proteína-ADN. Los resultados claves de este estudio son: en primer lugar que la presencia o ausencia del dominio regulatorio, jugaría un rol en la especificidad del reconocimiento proteína-ADN. En segundo lugar, la región espaciadora no aportaría especificidad a la unión, pero sí jugaría un papel clave en cuanto a la estabilidad de la unión. Y finalmente se concluye que Rob presenta dos modos de unión alternativos en donde presenta contacto directo con el surco mayor del ADN a través de la hélice 3 y la hélice 6 o bien interactúa principalmente sólo con caja A a través de hélice 3.
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    Andrographolide activates the canonical Wnt signalling pathway by a mechanism that implicates the non-ATP competitive inhibition of GSK-3 beta: autoregulation of GSK-3 beta in vivo
    (2015) Tapia Rojas, C.; Schüller, Andreas; Lindsay, C. B.; Ureta, R. C.; Mejias Reyes, C.; Hancke, J.; Melo Ledermann, Francisco Javier; Inestrosa Cantín, Nibaldo
    Wnt/β-catenin signalling is an important pathway that regulates multiple biological processes, including cell adhesion and determination of cell fate during animal development; in the adult nervous system it regulates the structure and function of synapses. Wnt-signalling dysfunction is associated with several neurodegenerative diseases such as schizophrenia and Alzheimer's disease. The use of natural compounds is an interesting strategy in the search for drugs with the therapeutic potential to activate this signalling pathway. In the present study, we report that andrographolide (ANDRO), a component of Andrographis paniculata, is a potent activator of Wnt signalling. Our results indicate that ANDRO activates this pathway, inducing the transcription of Wnt target genes by a mechanism that bypasses Wnt ligand binding to its receptor. In vitro kinase assays demonstrate that ANDRO inhibits glycogen synthase kinase (GSK)-3β by a non-ATP-competitive, substrate-competitive mode of action. In silico analyses suggest that ANDRO interacts with the substrate-binding site of GSK-3β. Finally, we demonstrated that the increase seen in the levels of GSK-3β phosphorylated at Ser9 is the result of an autoregulatory mechanism of the kinase in vivo, although not through activation of protein phosphatase type 1. Our results suggest that ANDRO could be used as a potential therapeutic drug for disorders caused by Wnt-signalling dysfunction such as neurodegenerative diseases.
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    Assessment of Mutations Associated With Genomic Variants of SARS-CoV-2: RT-qPCR as a Rapid and Affordable Tool to Monitoring Known Circulating Variants in Chile, 2021
    (2022) Angulo, J.; Martinez Valdebenito, C.; Pardo Roa, C.; Almonacid, L. I.; Fuentes Luppichini, E.; Contreras, A. M.; Maldonado, C.; Le Corre, N.; Melo Ledermann, Francisco Javier; Medina, R. A.; Ferrés, M.
    Since the first report of SARS-CoV-2 infection in humans, the virus has mutated to develop new viral variants with higher infection rates and more resistance to neutralization by antibodies elicited after natural SARS-CoV-2 infection or by vaccines. Therefore, rapid identification of viral variants circulating in the population is crucial for epidemiological assessment and efforts to contain the resurgence of the pandemic. Between January and November 2021, we performed a large variant RT-qPCR-based screening of mutations in the spike protein of 1851 SARS-CoV-2-positive samples derived from outpatients from the UC-Christus Health Network in Chile. In a portion of samples (n = 636), we validated our RT-qPCR-pipeline by WGS, obtaining a 99.2% concordance. Our results indicate that from January to March 2021 there was a dominance of non-identifiable variants by the RT-qPCR-based screening; however, throughout WGS we were able to identify the Lambda (C.37) variant of interest (VOI). From March to July, we observed the rapid emergence of mutations associated with the Gamma variant (P.1), which was quickly replaced by the appearance of a combination of samples harboring mutations associated with the Delta variant (B.1.617.2), which predominated until the end of the study. Our results highlight the applicability of cost-effective RT-qPCR-based screening of mutations associated with known variants of concern (VOC), VOI and variants under monitoring (VUM) of SARS-CoV-2, being a rapid and reliable tool that complements WGS-based surveillance.
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    Autosomal STR allele frequencies for the CODIS system from a large random population sample in Chile
    (2012) Vergara, I. A.; Villouta, P.; Herrera, S.; Melo Ledermann, Francisco Javier
    The thirteen autosomal STR loci of the CODIS system were typed from DNA of 732 unrelated male individuals sampled from different locations in Chile. This is the first report of allele frequencies for the thirteen STRs loci defined in the CODIS system from the Chilean population.
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    Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions
    (2019) Ribeiro, J.; Ríos Vera, C.; Melo Ledermann, Francisco Javier; Schüller, Andreas
    Summary Intra- and intermolecular contact surfaces are routinely calculated for a large array of applications in bioinformatics but are typically approximated from differential solvent accessible surface area calculations and not calculated directly. These approximations do not properly take the effects of neighboring atoms into account and tend to deviate considerably from the true contact surface. We implemented an extension of the original Shrake-Rupley algorithm to accurately estimate interatomic contact surface areas of molecular structures and complexes. Our extended algorithm is able to calculate the contact area of an atom to all nearby atoms by directly calculating overlapping surface patches, taking into account the possible shielding effects of neighboring atoms. Here, we present a versatile software tool and web server for the calculation of contact surface areas, as well as buried surface areas and solvent accessible surface areas (SASA) for different types of biomolecules, such as proteins, nucleic acids and small organic molecules. Detailed results are provided in tab-separated values format for analysis and Protein Databank files for visualization. Direct contact surface area calculation resulted in improved accuracy in a benchmark with a non-redundant set of 245 protein–DNA complexes. SASA-based approximations underestimated protein–DNA contact surfaces on average by 40%. This software tool may be useful for surface-based intra- and intermolecular interaction analyses and scoring function development. Availability and implementation A web server, stand-alone binaries for Linux, MacOS and Windows and C++ source code are freely available from http://schuellerlab.org/dr_sasa/. Supplementary information Supplementary data are available at Bioinformatics online.
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    Characterization of small RNAs in X. tropicalis gastrulae
    (2012) Faunes Quinteros, Fernando Emerson; Almonacid, L. I.; Melo Ledermann, Francisco Javier; Larraín Correa, Juan Agustín
    Here, we report and characterize deep sequencing data and bioinformatics analysis of small RNAs from X. tropicalis gastrula. A total of 17,553,124 reads with perfect match to the genome derived from 2,616,053 unique sequences were identified. Seventy-seven percent of theses sequences were not found in previous reports from X. tropicalis oocytes and somatic tissues. Bioinformatics analyses indicate that a large fraction of the small RNAs are PIWI-interacting RNAs. Up to 23.9% of small RNAs mapped to transposable elements and 27% to genic regions. Most of the abundant transposon-derived small RNAs are found in oocyte and gastrula libraries, suggesting that transposons also need to be silenced during early embryonic development. Importantly, novel clusters of piRNAs whose expression is activated after zygotic transcription begins were identified in the genome of X. tropicalis. Additionally, miRNAs were also identified and many of them are not present in oocytes, suggesting that miRNA expression is stage-specific. To the best of our knowledge, this is the first high throughput data release and bioinformatics characterization of small RNAs during Xenopus early embryonic development. genesis 50:572–58, 2012. © 2012 Wiley Periodicals, Inc.
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    Cloning and characterization of the genes encoding the high-affinity iron-uptake protein complex Fet3/Ftr1 in the basidiomycete Phanerochaete chrysosporium
    (2007) Larrondo Castro, Luis Fernando; Canessa, P.; Melo Ledermann, Francisco Javier; Polanco, R.; Vicuña, Rafael
    MCO1, a multicopper oxidase from Phanerochaete chrysosporium exhibiting strong ferroxidase activity, has recently been described. This enzyme shows biochemical and structural similarities with the yeast Fet3p, a type I membrane glycoprotein that efficiently oxidizes Fe(II) to Fe(III) for its subsequent transport to the intracellular compartment by the iron permease Ftr1p. The genome database of P. chrysosporium was searched to verify whether it includes a canonical fet3 in addition to mco1, and single copies of fet3 and ftr1 orthologues were found, separated by a divergent promoter. Pc-fet3 encodes a 628 aa protein that exhibits overall identities of about 40 % with other reported Fet3 proteins. In addition to a secretion signal, it has a C-terminal transmembrane domain, characteristic of these cell-surface-attached ferroxidases. Structural modelling of Pc-Fet3 revealed that the active site has all the residues known to be essential for ferroxidase activity. Pc-ftr1 encodes a 393 aa protein that shows about 38 % identity with several Ftr1 proteins from ascomycetes. Northern hybridization studies showed that the mRNA levels of both genes are reduced upon supplementation of the growth medium with iron, supporting the functional coupling of Fet3 and Ftr1 proteins in vivo.
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    Comparative protein structure modeling of genes and genomes
    (2000) Martí-Renom, M. A.; Stuart, A. C.; Fiser, A.; Sánchez, R.; Melo Ledermann, Francisco Javier; Sali, A.
    Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target–template alignment, model building, and model evaluation. The number of protein sequences that can be modeled and the accuracy of the predictions are increasing steadily because of the growth in the number of known protein structures and because of the improvements in the modeling software. Further advances are necessary in recognizing weak sequence–structure similarities, aligning sequences with structures, modeling of rigid body shifts, distortions, loops and side chains, as well as detecting errors in a model. Despite these problems, it is currently possible to model with useful accuracy significant parts of approximately one third of all known protein sequences. The use of individual comparative models in biology is already rewarding and increasingly widespread. A major new challenge for comparative modeling is the integration of it with the torrents of data from genome sequencing projects as well as from functional and structural genomics. In particular, there is a need to develop an automated, rapid, robust, sensitive, and accurate comparative modeling pipeline applicable to whole genomes. Such large-scale modeling is likely to encourage new kinds of applications for the many resulting models, based on their large number and completeness at the level of the family, organism, or functional network.
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    Comparison of different melting temperature calculation methods for short DNA sequences
    (2005) Panjkovich, A.; Melo Ledermann, Francisco Javier
    Motivation: The overall performance of several molecular biology techniques involving DNA/DNA hybridization depends on the accurate prediction of the experimental value of a critical parameter: the melting temperature Tm. Till date, many computer software programs based on different methods and/or parameterizations are available for the theoretical estimation of the experimental Tm value of any given short oligonucleotide sequence. However, in most cases, large and significant differences in the estimations of Tm were obtained while using different methods. Thus, it is difficult to decide which Tm value is the accurate one. In addition, it seems that most people who use these methods are unaware about the limitations, which are well described in the literature but not stated properly or restricted the inputs of most of the web servers and standalone software programs that implement them. Results: A quantitative comparison on the similarities and differences among some of the published DNA/DNA Tm calculation methods is reported. The comparison was carried out for a large set of short oligonucleotide sequences ranging from 16 to 30 nt long, which span the whole range of CG-content. The results showed that significant differences were observed in all the methods, which in some cases depend on the oligonucleotide length and CG-content in a non-trivial manner. Based on these results, the regions of consensus and disagreement for the methods in the oligonucleotide feature space were reported. Owing to the lack of sufficient experimental data, a fair and complete assessment of accuracy for the different methods is not yet possible. Inspite of this limitation, a consensus Tm with minimal error probability was calculated by averaging the values obtained from two or more methods that exhibit similar behavior to each particular combination of oligonucleotide length and CG-content class. Using a total of 348 DNA sequences in the size range between 16mer and 30mer, for which the experimental Tm data are available, we demonstrated that the consensus Tm is a robust and accurate measure. It is expected that the results of this work would be constituted as a useful set of guidelines to be followed for the successful experimental implementation of various molecular biology techniques, such as quantitative PCR, multiplex PCR and the design of optimal DNA microarrays. Availability: A binary software distribution to calculate the consensus Tm described in this work for thousands of oligonucleotides simultaneously for the LINUX operating system is freely available upon request to the authors or from our website http://protein.bio.puc.cl/melting-temperatures.html Contact: fmelo@bio.puc.cl Supplementary information: The large set of oligonucleotides, the detailed results of the comparative and accuracy benchmarks, and hundreds of comparative graphs generated during this work are available at our website http://protein.bio.puc.cl/melting-temperatures.html