Tools For the Bench

These links contain programs which can create restriction enzyme maps for your sequence of interest. Also included are tools for the design of oligonucleotide probes and PCR primers.

Found 80 links

Displaying 15 links

Bioinformatics ToolkitTool Content

Share This Link

This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

chipDTool Content

Share This Link

chipD is a web server that facilitates the design of DNA oligonucleotide probes for high-density tiling arrays. The algorithm ensures probe specificity, thermodynamic properties amongst probe sets and target sequence coverage.

This content is being maintained by ydufour.

CHOPCHOPTool Content

Share This Link

CHOPCHOP is a web tool for selecting the optimum target sites for CRISPR/Cas9- or TALEN-directed mutagenesis. It can be run with three basic input options, or with additional advanced parameters. The basic input comprises: (i) a gene name, genomic coordinates or a pasted sequence (accepting RefSeq, ENSEMBL, FlyBase and WormBase gene IDs); (ii) a growing list of organisms (including human, mouse, zebrafish, etc.); and (iii) the choice between CRISPR/Cas9 or TALEN mode.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

CODEHOPTool Content

Share This Link

COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.

DEQORDatabase Content

Share This Link

Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high silencing capacity.

dnaMATETool Content

Share This Link

dnaMATE calculates a consensus melting temperature (Tm) for any given short DNA sequence (16-30 nts) based on three independent thermodynamic data tables. Stand-alone version available; list of other melting temperature calculation servers also provided.

dsCheckTool Content

Share This Link

dsCheck takes a nucleotide sequence as input and estimates off-target effects caused by dsRNA (double-stranded RNA) employed in RNAi studies. dsCheck can be used either to verify previously designed dsRNA sequences, or to design off-target minimized dsRNAs.

DyNAVacSTool Content

Share This Link

DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences.

E-RNAiTool Content

Share This Link

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

EBI ToolsTool Content

Share This Link

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies. Example tools include those to compute sequence similarity searches, pairwise/multiple sequence alignment and protein functional analysis.

eBioinformaticsResource Content

Share This Link

This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.

links directory index: not available
TitlePublication YearGoogle Scholar Citation Count

Associated Tag Cloud