Software
Papel DrumPID
Watch the detailed tutorial.
YANAvergenz
Latest version of the YANA software, cited: Liang C, Liebeke M, Schwarz R, Zühlke D, Fuchs S, Menschner L, Engelmann S, Wolz C, Jaglitz S, Bernhardt J, Hecker M, Lalk M, Dandekar T.Staphylococcus aureusPhysiological growth constraints: insights from proteome-based flux calculations and external metabolite data. proteomics. May 2011; 11(10):1915-1935.
Comparing proteomics and metabolomics gives us a better understandingStaphylococcus aureusphysiological growth. For three of them, we updated genomic and proteomic information and provided strain-specific metabolic modelsS aureusStrains (COL, N315 and Newman). We found some differences in metabolism and enzymes. Growth experiments (using glucose or combined with oxygen restriction) were performed to measure external metabolites. From these data, the central metabolic fluxes were calculated with few errors. In the exponential phase, glycolysis is active and amino acids are used for growth. In later stages, dehydroquinate synthetase is suppressed and acetate metabolism begins. There are strain-specific differences for these stages. A time series of 2D gel protein expression data in strain COL yielded a second data set (glucose restriction) from which fluxes were calculated. The comparison with the predicted metabolite fluxes generally shows a good correlation. Outliers indicate different regulated enzymesS aureusCOL under these restrictions. In exponential growth, some enzymes in the upper glycolytic and pentose phosphate pathways have less activity and some enzymes in the lower glycolytic pathway are more active. In the transition phase, aspartate kinase is expressed to meet amino acid requirements, and in later phases there is high expression of glyceraldehyde-3-phosphate dehydrogenase and lysine synthetase. The fluxes of central metabolites and the protein expression of their enzymes are correlatedS aureus.
To download
YANAvergence is a major extension of the YANAsquare software that allows the integration of more experimental data to study the adaptation of the metabolic network under different conditions and loads.
YANAsquare GUI software package-To download
Requirement: Windows/Linux/Mac system with MASS libraries installed.
Tutorials and additional files.for flow calculation:
1. List of Processes in the Trunk Specific Models and Comparison:suppl_1_procesos.xls
2. Tutorial on how to use the YANAvergence program:yanavergence_demo.rar
3. Proteomic Data Set:suppl_2_proteineas.pdf
4. Condensed Model in SBML Format:suppl_0_sac_model.sbml
previous versions
-Software YANAcuadrado:To download
-Software is:To download
-Metaherramienta:To download
BMC Bio-informatics. 1. June 2005; 6:135.YANA: a software tool for the analysis of flow modes, gene expression and enzyme activities.Schwarz R, Musch P, von Kamp A, Engels B, Schirmer H, Schuster S, Dandekar T. Department of Bioinformatics, Biozentrum, University of Würzburg, Germany.
BACKGROUND: Over the years, several algorithms have been developed for steady-state analysis of metabolic networks. Elemental modal analysis (EMA) has proven to be particularly useful. Despite its poor usability, METATOOL has so far been the tool of choice as a reliable, powerful implementation of the algorithm. As reported here, the analysis of metabolic networks has been improved with a metabolic flow mode analyzer and editor. Of particular interest are analysis routines for expression levels and the most central and best connected metabolites and their metabolic connections. RESULTS: YANA presents a dedicated and cross-platform toolbox for metabolic networks with a graphical user interface for computing (integrating METATOOL), editing (including support for the SBML format), visualizing, centralizing and comparing elementary flow modes. In addition, YANA calculates the expected flux distributions for a given Elemental Mode (EM) activity pattern and vice versa. In addition, a dissection algorithm, a centralization algorithm, and an average diameter routine can be used to simplify and analyze complex networks. Proteomic or gene expression data give a rough indication of some individual enzyme activities, while the full flux distribution in the network is often not known. Because this data is noisy, YANA has a fast evolution algorithm (EA) for predicting EM activities with minimal errors, including warnings for inconsistent experimental data. We offer the option to include other known constraints (e.g. growth constraints) in the EA calculation process. The redox metabolism around glutathione reductase serves as a clear example. CONCLUSIONS: A graphical toolbox and editor for METATOOL and a set of additional routines for metabolic network analysis represent new user-friendly software for such efforts.
VeSelect a 3D Art
Automated 3D reconstruction tool for vesicle structures from electron tomograms
Automated image reconstruction is essential to cope with the constant increase of data from modern microscopy. We describe here the Fiji 3D ART VeSelecT macro that we developed to study synaptic vesicles in electron tomography. We used this tool to quantify vesicle properties (i) in the embryonic Danio rerio 4 and 8 days post fertilization (dpf) and (ii) to determine the neuromuscular N2 junctions (NMJs) of wild-type Caenorhabditis elegans and to compare his mutant. Septin (unc-59 (e261)). We show developmentally and mutant-specific changes in synaptic vesicle pools in both models. We confirmed the functionality of our macro by applying our 3D ART VeSElect in the zebrafish NMJ and showed smaller vesicles in 8 dpf and after 4 dpf embryos, which was validated by manual reconstruction of the vesicle pool. We further analyzed the influence of the C. elegans mutant septin unc-59(e261) on vesicle cluster formation and vesicle size. Automated recording and characterization of vesicles has been implemented in Fiji in two macros (recording and measuring). In particular, this flexible checking allows for the reduction of false positives through an optional manual verification step. Pre-processing and contrast enhancement work on image stacks at 1 nm/pixel in x and y direction. A semi-automatic cell sorting was integrated. 3D ART VeSelecT removes interfering components, detects vesicles using 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are captured in color with the RoiManager plugin, including the ability to manually remove mismatched confusion bubbles. The detailed assessment took into account performance (recognized vesicles) and specificity (true vesicles), as well as precision and recovery. In addition, we show a gain in morphological segmentation and filtering compared to learning-based methods and a large time gain compared to manual segmentation. 3D ART VeSelecT has low error rates and the speed gain can be up to 68 times faster compared to manual annotation. Both automatic and semi-automatic modes are explained, including a tutorial.
Detailed description and download can be found atHere
classificatiemacro
Synaptic vesicles (SVs) are a key component of neuronal signaling and perform different functions depending on their composition. On electron micrographs of neurites, two types of vesicles can be distinguished based on morphological criteria: the classical "clear core" (CCV) vesicles and the "dense core" (DCV) vesicles, generally larger, with differences in density. electronics because of their different charges. . Compared to CCVs, the exact role of DCVs is less well defined. DCVs are known to store neuropeptides that act as neuronal messengers and modulators. InC. elegans, They play a role in locomotion, perennial formation, oviposition, and mechano- and chemo-sensation. Another type of DCV, known as granule vesicles, is known to transport bassoon, piccolo, and other components of presynaptic density in the center of the active zone (AZ), and is therefore important for synaptogenesis.
To better understand the role of the different types of SVs, here we present a new automated approach to classify vesicles and quantify their properties using electron tomography. We combine machine learning with an extension of our previously developed vesicle segmentation workflow, the ImageJ macro 3D ART VeSElect, to reliably distinguish CCV and DCV using image-based functions. We applied this method to electron tomograms of theC. elegansNMJ and find a higher proportion of DCV and a greater mean distance between DCV and AZ in larvae present compared to adult hermaphrodites. Our machine learning approach could be applied to study the properties of different groups of synaptic vesicles in electron tomograms of different model organisms.
Download the trial software and data:
Updated version of 3D ART VeSelecT
classificatiemacro
Test dates
User descriptions:
How to use the classification macro
How to use a Python script to retrain the algorithm
J Chem Inf Comput Sci. 2002 maart-april; 42(2):405-7.
A versatile structure domain analysis server that uses profile weight matrices.
Schmidt S, Bork P, Dandekar T.
EMBL, PO Box 102209, D-69012 Heidelberg, Germany.
The WEB tool "AnDom" maps all experimentally determined structural domains contained within a given protein sequence, including large and multidomain proteins. The server uses profile-specific arrays of user-defined multi-sequence alignments of all known SCOP domains (SCOP version 1.75 updated). The prediction time is short, enabling numerous applications for structural genomics, including the study of complex families of eukaryotic proteins.
PMID: 11911710 [PubMed - indexed to MEDLINE]
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441490/
nucleic acids res. 32 (web server issue): W154-9.
Riboswitch Finder: A tool for identification of riboswitch RNA.
Bengert P, Dandekar T.
Biochemistry Center, Project Group B2 (Dandekar/Schirmer), University of Heidelberg, Im Neuenheimer Feld 504, 69120 Heidelberg, Germany.
We describe a dedicated RNA motif search program and web server for identifying RNA riboswitches. The Riboswitch Finder analyzes a given sequence via the web interface, verifies specific sequence elements and secondary structures, calculates and displays the energy folding of the RNA structure, and performs a series of tests that include this information to determine whether the motifs (or variants) Depending on the species of Bacillus subtilis, several highly sensitive riboswitches are present in the given RNA sequence. Determination in batch mode (all series entered at once and separated by FASTA format) is also possible.
The program is included and is available as local software for internal installation and as a web serverhttp://riboswitch.bioapps.biozentrum.uni-wuerzburg.de.
PMCID: PMC441490
PMID: 15215370 [PubMed - indexed to MEDLINE]
http://nar.oxfordjournals.org/content/31/13/3441.long
nucleinezuren res. July 1, 2003; 31(13):3441-5.
A software toolbox for analyzing RNA regulatory elements.
Bengert P, Dandekar T.
Parasitology, Universiteit van Heidelberg, Im Neuenheimer Feld 324, 69120
Heidelberg, Germany.
We describe an integrated toolbox for identifying RNA regulatory elements. The RNA analyzer collects general and specific information about each RNA sequence or set of sequences submitted in FASTA format. Rapidly identifies and scans the different regions of an RNA (including 5'-UTR, CDS, 3'-UTR in mRNA) looking for specific RNA signals (in each of these regions e.g. polyA site, AU rich region etc .). 3'UTR). Performs a rapid RNA folding routine to provide an overview of RNA folding. In addition, the content of the structure, the folding energy and the stem are analyzed.
Grind. In addition, consensus templates are used to determine whether functional structures for translational control (template: IRE), structured RNA (template: tRNA consensus), or catalytic RNA (template: trans-splice RNA) are present and provide clues about how well, are the found structures consistent with these templates.
PMCID: PMC168974
PMID: 12824342 [PubMed - indexed to MEDLINE]
http://www.biomedcentral.com/1471-2105/7/461
BMC Bio-informatics. 20 October 2006; 7:4
inGeno: An integrated genome and orthologue viewer to improve genome-to-genome comparisons.
Liang C, Dandekar T.
Department of Bioinformatics, Biozentrum, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany. liang@biozentrum.uni-wuerzburg.de
BACKGROUND: Systematic genome comparisons are an important tool for uncovering genetic functions, pathogen properties, metabolic pathways, and genome evolution in the post-genomics era. In addition, these comparisons provide important clues for vaccine and drug development. Existing genome comparison software often lacks accurate information on orthologs, the function of identified similar genes, and genome-wide reports and lists of specific functions. All this additional functionality and analysis is provided here in the context of a modular "inGeno" software tool written in Java with Biojava subprograms.
RESULTS: InGeno provides an easy-to-use interactive visualization platform for sequence comparisons (reciprocal protein integral comparisons) between whole genome sequences and all associated annotations and features. Comparative data can be collected in flexible formats from a variety of different sequence analysis programs. Automated scatterplot analysis includes result reduction, filtering, orthologous testing, and linear regression, followed by intelligent clustering (local collinear blocks; LCBs) to reveal similar genomic regions. In addition, the system provides an editor for viewing and aligning the genome, collinear relationships, and strain-specific islands. Annotations and specific features are analyzed, recognized, grouped, logically linked, displayed and summarized in reports.
CONCLUSIONS: As demonstrated in this study, inGeno in particular can be used to inter-study and compare prokaryotic genomes (gram positive and negative, as well as near and distant species) and has been shown to be sensitive and accurate. This modular software is easy to use and easy to adapt to new routines to meet specific custom needs.
PMCID: PMC1635569
PMID: 17054788 [PubMed - indexed to MEDLINE]
http://www.ncbi.nlm.nih.gov/pubmed/?term=dandekar-T+ingeno
Prof. Dist.
Motivation:Profile Neighbor Joining (PNJ), as implemented in ProfDist, is computationally efficient for restoring very large trees. In addition to the vast amount of sequence data, structure is important in RNA alignment analysis and phylogenetic reconstruction.
Results:For this purpose, ProfDistS provides a phylogenetic framework that uses individual secondary RNA structures to reconstruct phylogenies from sequence-structure alignments using Profile Neighbor Joining (PNJ) with manual or iterative and automatic profiling. In addition, ProfDistS can also work with protein sequences.
Availability:ProfDistS is available free for non-commercial use for Windows, Linux and MAC operating systems athttp://profdist.bioapps.biozentrum.uni-wuerzburg.de.
Contact: Tobias Mueller,Matthew Wolf.
L1Basis
http://nar.oxfordjournals.org/content/33/suppl_1/D498.long
nucleïnezuren res. 33 (databaseprobleem): D498-500.
L1Base: from functional annotation to prediction of active LINE-1 elements.
Penzkofer T, Dandekar T, Zemojtel T.
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany.
L1Base is a special database of putative active LINE-1 (L1) inserts found in the human and rodent genomes that are: (i) intact in both open reading frames (ORFs), full-length L1 (FLI-L1) and ( ii) ORF2 intact but ORF1 altered (ORF2-L1). In addition, non-intact full-length (>6000 bp) L1 (FLnI-L1) has also been used for their regulatory potential
included in the database. Application of a new annotation method, L1Xplorer, allowed detailed annotation of functional sequence features important for L1 activity, such as B. Transcription factor binding sites and amino acid residues.
L1Base is available online at http://l1base.molgen.mpg.de. In addition, access to the data stored in the database is possible via a DAS service (http://l1das.molgen.mpg.de:8080/das) in Ensembl's web browser.
PMCID: PMC539998
PMID: 15608246 [PubMed - indexed to MEDLINE]
CBCA-Analysator
In Silico Biol.2005;5(3):291-4. Electronic release March 16, 2005.
CBCAnalyzer: Infer phylogenies based on basic compensatory changes in RNA secondary structures.
Wolf M, Friedrich J, Dandekar T, Müller T.
Department of Bioinformatics, Biozentrum, University of Würzburg, Am Hubland,
D-97074 Wurzburg, Germany.
CBCAnalyzer (CBC = Compensatory Base Change) is a custom-written software toolkit consisting of three parts: CTTransform, CBCDetect, and CBCTree. CTTransform reads various CT file formats and outputs the bracket-dot-bracket format, which is typically used as an input to other tools such as RNAforester, RNAmovie, or MARNA. The latter creates a multiple alignment based on primary sequences and secondary structures, which can now be used as input to CBCDetect. CBCDetect counts the total number of CBCs with all sequences aligned.
This is important to identify species that are discriminated against because of their sexual incompatibility. The count matrix (distance matrix) obtained from CBCDetect is used as input to CBCTree, which reconstructs a phylogram using the BIONJ algorithm. In this note we describe the functions of the toolbox and application examples. The toolbox provides a graphical user interface.
It is written in C++ and available for free at:http://cbcanalyzer.bioapps.biozentrum.uni-wuerzburg.de.
PMID: 15996120 [PubMed - Indexed to MEDLINE]
YANAcuadrado
http://www.biomedcentral.com/1471-2105/8/313
BMC Bioinformatics. August 28, 2007; 8:313. Reconstruction, visualization and analysis of integrated networks with YANAsquare. Schwarz R, Liang C, Kaleta C, Kühnel M, Hoffmann E, Kuznetsov S, Hecker M, Griffiths G, Schuster S, Dandekar T. Department of Bioinformatics, Biozentrum Am Hubland, D-97074 University of Würzburg, Germany. BACKGROUND: Modeling metabolic networks involves tasks such as network construction, network mapping, calculation of metabolic fluxes, and network robustness testing. RESULTS: YANAsquare provides a software framework for fast network construction (flexible path navigator with local or remote operation mode), network overview (YANAsquare editor and visualization routine), and network performance analysis (flow mode calculation, as well as objectivity and robustness). to test). YANAsquare is delivered as an easy to configure Java program package. It is fully compatible and integrates with the programs YANA (translation of gene expression values into current distributions, decomposition of metabolite networks) and Metatool (calculation of elementary mode). As application examples, we configured and modeled the phospholipid network in the phagosome- and genome-scale metabolic maps of S.aureus, S.epidermidis and S.saprophyticus and tested its robustness against enzymatic spoilage. CONCLUSION: YANAsquare is a software application for the rapid configuration, visualization and analysis of small, large and genomic metabolic networks. PMCID: PMC2020486
PMID: 17725829 [PubMed - indexed to MEDLINE]
ES
Original YANA version, which provides the ability to build a network and Amazon Logistics. to see
http://www.biomedcentral.com/1471-2105/6/135
BMC Bioinformatics. June 1, 2005; 6:135. YANA: a software tool for the analysis of flow modes, gene expression and enzyme activities. http://www.ncbi.nlm.nih.gov/pubmed/15929789 Schwarz R, Musch P, von Kamp A, Engels B, Schirmer H, Schuster S, Dandekar T. Department of Bioinformatics, Biozentrum, University of Wurzburg, Germany .
BACKGROUND: Over the years, several algorithms have been developed for steady-state analysis of metabolic networks. Elemental modal analysis (EMA) has proven to be particularly useful. Despite its poor usability, METATOOL has so far been the tool of choice as a reliable, powerful implementation of the algorithm. As reported here, the analysis of metabolic networks has been improved with a metabolic flow mode analyzer and editor. Of particular interest are analysis routines for expression levels and the most central and best connected metabolites and their metabolic connections.
RESULTS: YANA presents a dedicated and cross-platform toolbox for metabolic networks with a graphical user interface for computing (integrating METATOOL), editing (including support for the SBML format), visualizing, centralizing and comparing elementary flow modes. In addition, YANA calculates the expected flux distributions for a given Elemental Mode (EM) activity pattern and vice versa. In addition, a dissection algorithm, a centralization algorithm, and an average diameter routine can be used to simplify and analyze complex networks. Proteomic or gene expression data give a rough indication of some individual enzyme activities, while the full flux distribution in the network is often not known. Because this data is noisy, YANA has a fast evolution algorithm (EA) for predicting EM activities with minimal errors, including warnings for inconsistent experimental data. We offer the option to include other known constraints (e.g. growth constraints) in the EA calculation process. The redox metabolism around glutathione reductase serves as a clear example. All software and documentation can be downloaded atwww.biozentrum.uni-wuerzburg.de/bioinfo/computing/. CONCLUSIONS: A graphical toolbox and editor for METATOOL and a set of additional routines for metabolic network analysis represent new user-friendly software for such efforts.
PMCID: PMC1175843
PMID: 15929789 [PubMed - Indexed to MEDLINE]
platelet network
PlaquettesWebprovides a new systems biology workbench for the analysis of platelet signaling in the functional context of integrated networks. The database was created by combining data from recent platelet proteome and transcriptome (SAGE) studies with information on protein-protein interactions and kinase-substrate relationships from bioinformatics databases and from published literature. The mass spectrometry-based platelet phosphoproteome was combined with site-specific phosphorylation/dephosphorylation information from the Human Protein Database (HPRD), augmented with PhosphoSite data, and augmented by bioinformatic sequence analysis for site-specific kinase predictions. The integration of annotations on kinases, protein domains, transmembrane regions, gene ontology, disease associations and drug targets provides comprehensive functional tools for platelet signaling analysis. The use of graphical visualization for specific subnetworks allows the study of key signaling modules involved in platelet activation and inhibition. By integrating different sources of information and high curation standards, PlateletWeb provides the biological background of systems for signal transduction research in human platelets. When using information from this source, please cite the following publication:
ETV
A Java applet for exploring the new top-level classification of eukaryotes with a focus on protist taxonomy
4VENTA
http://www.biomedcentral.com/1471-2105/7/498
BMC Bio-informatica. 13 november 2006; 7:498.
4SALE: A tool for synchronous RNA sequencing, alignment and editing of secondary structures.
Seibel PN, Müller T, Dandekar T, Schultz J, Wolf M.
Department of Bioinformatics, Biozentrum, University of Würzburg, Am Hubland,
Wurzburg, Germany.
BACKGROUND: In sequence analysis, multiple alignment forms the basis of all analyzes performed. Errors in an alignment can strongly influence all subsequent analysis and thus lead to incorrect predictions. Handmade and improved alignments are now necessary and common. In the case of RNA sequences, the primary sequence and an agreed upon secondary structure, e.g. B. the cloverleaf structure of tRNA is known. Recently, some alignment editors have been proposed that can integrate and model both types of information. However, with the advent of a large number of reliable RNA sequences along with their resolved secondary structures (available e.g. in the ITS2 database), we are faced with the problem of processing sequences and their associated secondary structures synchronously.
RESULTS: 4SALE fills this gap. The application enables fast sequencing and synchronous alignment of secondary structures for large data sets, as well as synchronous manual editing of aligned sequences and their secondary structures for the first time. This study describes an algorithm for the synchronous alignment of sequences and the associated secondary structures, as well as the main features of 4SALE that are used for further analysis and editing. 4SALE creates a unique and optimal starting point for any RNA sequence and structure analysis.
CONCLUSION: 4SALE offers an intuitive and user-friendly interface and is a comprehensive toolbox for RNA analysis based on secondary structure and sequence information. The program combines structure and sequence databases such as the ITS2 database with phylogeny programs such as the CBCAnalyzer. 4SALE is written in JAVA and is therefore platform independent.
The software is available free of charge and is distributed via the website http://4sale.bioapps.biozentrum.uni-wuerzburg.de.
PMCID: PMC1637121
PMID: 17101042 [PubMed - indexed to MEDLINE]
A tool for aligning and editing synchronous RNA sequences and secondary structures
ITS2-database
Metatool is a C program developed between 1998 and 2000 by Thomas Pfeiffer in collaboration with Juan Carlos Nuno (Madrid), Stefan Schuster and Ferdinand Moldenhauer (Berlin). It serves to draw conclusions about the structure of metabolic network pathways from stoichiometric reaction equations and information about the reversibility and irreversibility of enzymes. Algorithm describedHere.
Friedrich Schiller University Jena
Isotope
Isotope is an easy-to-use platform for Massive Isotopomer Distribution Analysis (MIDA), a technique that enables the determination of metabolic fluxes based on labeling experiments with 13C-enriched precursors. It is designed with simple and robust data management to quantify isotopomeric populations in 13C-labeled amino acid mixtures. It is capable of processing experimental data (GC-MS), estimating mass values and predicting natural quantities, relative quantities and fractional molar quantities.
Isotopo provides the new standardization of experimental data with a database and file-based recording system for efficient data manipulation and management. It also provides a dedicated data classifier (IDC) based on guided machine learning principles that enables automatic extraction, classification and standardization of isotopomer data (from Excel spreadsheets). It is developed using software engineering principles, implemented in Microsoft Visual Studio Dot Net (C#) according to design patterns for human-computer interaction, and is well tested internally.
LS-MASS
The Least Squares Isotopomer Mass Distribution Analyzer (LS-MIDA) is an application developed to estimate isotopomer mass distribution from spectral data by analyzing a particular mass peak and mass atomic fragment. It is able to analyze raw experimental data based on labeled (isotopic) (carbon) metabolites (various amino acids). Estimate mass values (minimum and maximum), predict theoretical values for pure compounds, plot linear relationships between masses within a compound's range, and perform linear regression analysis to predict relative intensity values with respect to each mass. charge ratio. To allow a better understanding of the results obtained, LS-MIDA visualizes the results by drawing a spectrometer.
To download
ADAM
Integrated intelligent data management for modeling and monitoring pathophysiological cascades in thrombosis and hemostasis. This research aims to conceive and support the medical community with the proposal and implementation of an innovative initiative that addresses key challenges that consist of best managing a specific diagnosis, acting quickly in emergency situations, protecting personal data and combining individual patient data with common repositories. . Enable therapy monitoring and analysis of individual variations against gold standard therapy guidelines with a proposal for an integrated, high-performance product data management solution, expecting broad adoption by the European/international industry for better data analysis, efficient management and global exploitation.
genomic properties
Molecular sequencing techniques help to understand microbial biodiversity in terms of species richness, structural structure and function. In this context, barcoding, metabarcoding, genomics and metagenomics are available as methods. The first two are limited to taxonomic assignments, while genomics is only concerned with the functional capabilities of a single organism. Metagenomics, on the other hand, provides information about the organic and functional diversity of a community. However, it is currently very demanding in terms of labor and cost, and therefore not applicable to most laboratories. Here we show in a proof-of-concept that computational approaches can store functional information about microbial communities, assessed by 16S rDNA (meta)barcoding by referencing reference genomes. We developed an automated process to demonstrate that such integration can derive preliminary or additional genomic content from a community. We applied it to two biological datasets and delineated significantly overrepresented protein families across communities.
Reference:
Keller A, Horn H, Förster F, Schultz J. Computational integration of genomic traits in 16S rDNA microbiota sequencing studies. Gene. July 30, 2014. pii: S0378-1119(14)00890-7. doi: 10.1016/j.gene.2014.07.066. PubMed PMID: 25084126.