DNA Learning Center Home DNA Learning Center Preparing students and families to thrive in the gene age Catalog People Learning Resource Type Alignments PRALINE - is a multiple sequence alignment program with many options to optimize the information for each of the input sequences; e.g. global or local preprocessing, predicted secondary structure information and iteration capabilities. (Reference: V.A. Simossis et al. (2005) Nucleic Acids Res. 33: 816-824). A similar type of output can be obtained using SPEM (Laboratory of Biophysics & Bioinformatics, University of Buffalo, U.S.A.). Protein Data Bank - RCSB PDB A Structural View of Biology This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data. The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond. Use this website to access curated and integrated biological macromolecular information in the context of function, biological processes, evolution, pathways, and disease states. A Molecular View of HIV Therapy
Transcription (genetics) Simplified diagram of mRNA synthesis and processing. Enzymes not shown. Transcription can be reduced to the following steps, each moving like a wave along the DNA. Transcription has some proofreading mechanisms, but they are fewer and less effective than the controls for copying DNA; therefore, transcription has a lower copying fidelity than DNA replication.[2] As in DNA replication, DNA is read from 3' end → 5' end during transcription. Meanwhile, the complementary RNA is created from the 5' end → 3' end direction. Sequence Alignments Web Alignments are nucleotide and protein alignments that represent the fullest spectrum of sequences in the database. Filtered Web Alignments are a filtered subset of sequences from the web alignments. These alignments are cleaner, but contain slightly less information. Subtype Reference Alignments contain approximately 4 representatives of each subtype.
Figure 2 : C.Elegans: : Mining the functional genomic landscape : Nature Reviews Genetics a | Protocols for administering RNAi in C. elegans. b | Examples of RNAi phenotypes. Top, a control, wild-type embryo at the four-cell stage (left) and an mcm-5(RNAi) embryo showing altered nuclear appearance (right). The timing of cell divisions in this embryo is also abnormal (only one of the cells has divided a second time) after the first embryonic division. Middle, a wild-type, two-cell-stage embryo (left) and a F55H2.3(RNAi) embryo (right) showing vertical rather than horizontal orientation of the spindle pole bodies in the right-hand cell. White bars indicate orientation of the mitotic spindle. Bottom, a wild-type, two-cell-stage embryo (left) and a C16A3.9(RNAi) embryo with several meiotic defects (right).
Hepitope: HLA-Enriched Possible Epitope The Hepitope tool searches for hopeful-epitopes or "Hepitopes". The tool tests for HLA alleles that are enriched in a set of individuals that react with a set of peptides. This can be used in conjunction with ELF (Epitope Location Finder) to scan the peptides for known epitopes in the database and anchor motifs to help identify epitopes within a larger peptide fragment. See below for details about the input and output of the program. Input
RNA interference Lentiviral delivery of designed shRNA's and the mechanism of RNA interference in mammalian cells. RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression, typically by causing the destruction of specific mRNA molecules. Historically, it was known by other names, including co-suppression, post transcriptional gene silencing (PTGS), and quelling. Only after these apparently unrelated processes were fully understood did it become clear that they all described the RNAi phenomenon. Andrew Fire and Craig C. Mello shared the 2006 Nobel Prize in Physiology or Medicine for their work on RNA interference in the nematode worm Caenorhabditis elegans, which they published in 1998.
Genetically Modified Tomatoes These GM tomatoes, however, did not meet their expectations. Although they were approved in the US and several other countries, tomatoes with delayed ripening have disappeared from the market after peaking in 1998. At this point, no genetically modified tomatoes are being grown commercially in North America or in Europe. Genetically modified tomatoes are not approved in Europe. Real Time PCR Tutorial In real-time PCR using SYBR green binding to amplified cDNA, we are simply measuring the fluorescence increase as the dye binds to the increasing amount of DNA in the reaction tube. We hope that this increase in fluorescence is coming from the DNA that we wish to measure but some of the signal could come from DNA other than that which we are trying to amplify. Is there any way to check that the correct fragments were amplified? One way to do some checking of the products is to do a melting curve.
European Biotechnologist - Part 2 Bio-Rad Laboratories has recently published a paper discussing the analysis steps performed by HRM software to identify thermal profile differences and examine the effect of assay optimization techniques, temperature increments, and instrument selection on the ability to distinguish different genotypes using HRM analysis. The authors found that the most important steps for robust HRM analysis [...] High resolution melt (HRM) analysis is a relatively new technique used in detecting small variations in DNA sequences between varying populations. Important applications of HRM include SNP analysis, genotyping and methylation analysis. Sean Taylor, Field Application Specialist, Bio-Rad Laboratories, Canada, presented a 20 minute tutorial webinar on high resolution melt analysis and how to use [...] High resolution melt (HRM) analysis is a relatively new technique used in detecting small variations in DNA sequences between varying populations.
Compbio.mit.edu - MIT Computational Biology Group Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution.
Chromatin Immunoprecipitation Sequencing View Larger Image DNA enrichment by ChIP and SOLiD™ fragment library construction Comparison of ChIP Detection Platforms