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DNannotator is a tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user-defined annotations onto different versions of genomic sequences (<30Kb size limit).
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-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.
GeMprospector is designed to find cross-species genetic marker candidates in legumes and grasses. GeMprospector automates PCR primer design based on multiple sequence alignments of submitted ESTs and their homologues in sequence databases from legumes or grasses.
IDT SciTools is a suite of online tools for the analysis and design of DNA and RNA oligomers. Tools include those for selection of PCR primers, antisense oligonucleotides, or sequences for RNA interference, as well as tools for calculation of secondary structures.
MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5\' and 3\'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).
MutScreener is a human-specific primer design tool that considers gene annotation information to design primers for mutation screening. Users can provide custom gene annotation or use existing public gene annotations.
featured linkSYFPEITHIhttp://www.syfpeithi.de/SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. The database can be used to predict…