Oligo Explorer Download !FULL!
Kimbra Koran
OligoWalk is an online sever calculating thermodynamic features of sense-antisense hybidization. It predicts the free energy changes of oligonucleotides binding to a target RNA. It can be used to design efficient siRNA targeting a given mRNA sequence. The source code of OligoWalk for siRNA design can be downloaded from here.
The efficient siRNA selection method is described in a published paper (link). More references are listed in the Help page.
With all the different types of oligonucleotides, it is hard to select an oligo that fits best to your investigation and application.
Our interactive oligonucleotide decision tree will guide you to the best-fitting oligo for your project.
The crystal structure of oligo-1,6-glucosidase (dextrin 6-alpha-glucanohydrolase, EC 3.2.1.10) from Bacillus cereus ATCC7064 has been refined to 2.0 A resolution with an R-factor of 19.6% for 43,328 reflections. The final model contains 4646 protein atoms and 221 ordered water molecules with respective root-mean-square deviations of 0.015 A for bond lengths and of 3.166 degrees for bond angles from the ideal values. The structure consists of three domains: the N-terminal domain (residues 1 to 104 and 175 to 480), the subdomain (residues 105 to 174) and the C-terminal domain (residues 481 to 558). The N-terminal domain takes a (beta/alpha)8-barrel structure with additions of an alpha-helix (N alpha6') between the sixth strand Nbeta6 and the sixth helix N alpha6, an alpha-helix (N alpha7') between the seventh strand Nbeta7 and the seventh helix N alpha7 and three alpha-helices (N alpha8', N alpha8" and N alpha8'" between the eighth strand Nbeta8 and the eighth helix N alpha8. The subdomain is composed of an alpha-helix, a three-stranded antiparallel beta-sheet, and long intervening loops. The C-terminal domain has a beta-barrel structure of eight antiparallel beta-strands folded in double Greek key motifs, which is distorted in the sixth strand Cbeta6. Three catalytic residues, Asp199, Glu255 and Asp329, are located at the bottom of a deep cleft formed by the subdomain and a cluster of the two additional alpha-helices N alpha8' and N alpha8" in the (beta/alpha)8-barrel. The refined structure reveals the locations of 21 proline-substitution sites that are expected to be critical to protein thermostabilization from a sequence comparison among three Bacillus oligo-1,6-glucosidases with different thermostability. These sites lie in loops, beta-turns and alpha-helices, in order of frequency, except for Cys515 in the fourth beta-strand Cbeta4 of the C-terminal domain. The residues in beta-turns (Lys121, Glu208, Pro257, Glu290, Pro443, Lys457 and Glu487) are all found at their second positions, and those in alpha-helices (Asn109, Glu175, Thr261 and Ile403) are present at their N1 positions of the first helical turns. Those residues in both secondary structures adopt phi and phi values favorable for proline substitution. Residues preceding the 21 sites are mostly conserved upon proline occurrence at these 21 sites in more thermostable Bacillus oligo-1,6-glucosidases. These structural features with respect to the 21 sites indicate that the sites in beta-turns and alpha-helices have more essential prerequisites for proline substitution to thermostabilize the protein than those in loops. This well supports the previous finding that the replacement at the appropriate positions in beta-turns or alpha-helices is the most effective for protein thermostabilization by proline substitution.
Many researchers use Vector NTI as a major tool for storing and managing their laboratory experiment-related information. In order to generalize the Vector NTI database and make it suitable for a wider range of information management functions, Vector NTI allows you to associate User Fields with any database object (molecules, oligos, etc.). A User Field may contain any laboratory-specific and user-specific information necessary for an appropriate description of the object. User Fields can be imported, exported, displayed, printed and managed just as the regular database fields.
Check the Oligo & Peptides Filter box to filter search results based on homology between target molecules and given oligonucleotides and short peptides. The filter can be set up by pressing the Oligo & Peptides Setup button. The Conditions dialog will appear, allowing you to chose oligonucleotide and peptides for homology search.
The Keywords Filter allows you to filter search results based on keywords associated with an object. Only oligos that have any one of the keywords shown in the Keywords list box will be found by the search. Press the Add button to select from the list of existing keywords. To remove a keyword from the box after it has been added, select it and press the Remove button. To clear the Keywords box, press the Remove All button.
Use this operation to import molecules and oligonucleotides from a directory of text files. The files must be in the GenBank format (DNA/RNA molecules), GenPept format (protein molecules) or Vector NTI's oligo text format (oligonucleotides). You will be asked for the List File describing the objects you are going to import. When Vector NTI exports the objects into a directory of text files (see below) it automatically creates the appropriate List File.
Use this operation to export all objects of the specified subbase into a directory of text files. The files will be in GenBank (DNA/RNA molecules), GenPept (protein molecules) or Vector NTI's oligo text format (oligonucleotides). You will be asked for a name of the List File which Vector NTI will create to describe the objects you are importing.
To set a value for a User Field, select the User Field and choose a subset of database objects from the database tree. You may choose all database objects regardless of their type or a particular subbase for database objects of a particular type (molecules, enzymes, oligos or gel markers). If you don't want to overwrite existing values of the User Field in the selected group of objects, check the "Do not overwrite..." box.
To clear all values of a User Field, select the User Field and choose a subbase of database objects in the database tree. You may choose all database objects regardless of their type or a particular subbase for database objects of a particular type (molecules, enzymes, oligos or gel markers).
Vector NTI allows you to create and access special databases which may be used as repositories of DNA/RNA or protein molecules, enzymes, oligonucleotides, and gel markers shared between several Vector NTI users on a network. Shared databases give you the same flexibility and control as Vector NTI archives (including automatic consistency checks for constructed molecules) but they are much more convenient for groups of people which already use a computer network to exchange information and store common data.
GATExplorer (Genomic and Transcriptomic Explorer) is a database and web platform that integrates a gene loci browser with nucleotide level mappings of oligo probes from expression microarrays. It allows interactive exploration of gene loci, transcripts and exons of human, mouse and rat genomes, and shows the specific location of all mappable Affymetrix microarray probes and their respective expression levels in a broad set of biological samples. The web site allows visualization of probes in their genomic context together with any associated protein-coding or noncoding transcripts. In the case of all-exon arrays, this provides a means by which the expression of the individual exons within a gene can be compared, thereby facilitating the identification and analysis of alternatively spliced exons. The application integrates data from four major source databases: Ensembl, RNAdb, Affymetrix and GeneAtlas; and it provides the users with a series of files and packages (R CDFs) to analyze particular query expression datasets. The maps cover both the widely used Affymetrix GeneChip microarrays based on 3' expression (e.g. human HG U133 series) and the all-exon expression microarrays (Gene 1.0 and Exon 1.0).
To analyze transcriptomic data in a genomic context, GATExplorer integrates five datasets: (i) the human, mouse and rat genomes (derived from Ensembl ); (ii) the sequences and IDs of all oligonucleotide probes (perfect match only) from all Affymetrix expression microarrays for these species; (iii) de novo mapping data of each array probe to the transcriptome of the corresponding organism, with the genomic coordinates for each locus (including locations on exons, introns and across exon-exon junctions) and identification of any intersecting genes, transcripts and exons; (iv) mapping data of unmapped probes to transcripts in RNAdb (research.imb.uq.edu.au/RNAdb), a database of ncRNAs of human and mouse; and (v) detailed expression data derived from a set of microarrays from different cell types, tissues or organs (GeneAtlas GEO ID GSE1133 [6]) calculated at probe- and probeset-level using complete de novo mapping.
BLASTN sequence alignment was used to map the 25-mer oligo probes of the main Affymetrix expression microarrays to the RNA sequences of human, mouse and rat, selecting only complete perfect match alignments. The mapped probes were then placed in the corresponding genome based on the coordinates of the main genomic entities defined by Ensembl. The versions of the genomes assemblies and the source databases in current use are indicated on the website (PROBE MAPPING section, "Genomes ASSEMBLY and Databases VERSION").
The PROBE MAPPING section also presents details regarding the specific "Methods" used, the "Statistics" regarding the mapping to different transcribed entities and a "Comparative Analysis" with other related applications. The "Methods" page provides descriptions and links to the main data sources used in GATExplorer and a graphical schematic view of the pipeline followed to build the web platform, presenting the main steps and procedures applied and the files and packages provided by the server. The "Statistics" page provides the data derived from the sequence mapping of all the oligonucleotide probes from Affymetrix expression microarrays into different types of RNAs. Probes are classified as mapping to: protein-coding RNAs (mature mRNAs), non protein-coding RNAs (ncRNAs) or unassigned to any known RNA (NA). Probes that only map to introns were classified as mapping to putative ncRNAs. The percentage of probes mapping to each class is provided for four types of widely used human expression microarrays platforms. The page also provides statistics on the number and percentages of transcripts and genes mapped by the probes in each Affymetrix expression microarray (for human Homo sapiens, mouse Mus musculus and rat Rattus norvegicus); and the number and percentages of probes that map to transcripts and genes with respect to the total in each array. The "Comparative Analysis" page includes a comparison of GATExplorer with other related applications that have been previously published. The page examines four studies that have undertaken an alternative mapping of probes to genes for Affymetrix microarrays. Some of these re-mapping approaches and tools are limited to a subset of microarray platforms or do not apply to whole-transcript expression microarrays (i.e. Gene 1.0 and Exon 1.0). Among the previous studies, none present mapping to intronic regions or ncRNAs.
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