Produces degenerate primers for amplification and sequencing of short viral genomes. PriSM processes through three main steps for selecting and matching primers: make consensus, primer design and amplicon selection. This application can generate a panel of primer pairs that tile along the entire length of a viral genome. It can use a posteriori information of viral sequence databases to construct efficiently amplification primer pairs.
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Begins conservational analysis for PCR primer design at the protein level, allowing the user to design consensus primers capable of detecting homologous coding sequences even when low-to-moderate sequence information is available. CEMAsuite also condenses the wealth of information associated with multiple sequence alignments and presents them in an intuitive manner, allowing the user to quickly and effectively address degenerate primer design considerations. The goal of CEMAsuite is to aid in the design of minimum-degeneracy primer sets which are robust enough for the assay at hand, while retaining as much specificity and product homology as possible.
Represents a program based on an algorithm called weighted randomized combination for solving the maximum coverage degenerate primer design problem. DegePrime preserves the correlation structure among nucleotides. This tool can design primers based on over a million sequences. It can be useful to substantially improve the taxonomic coverage of a popular primer pair for amplification of the region of bacterial.
Employs suffix array methods for efficient calculations on oligos 10-100 nt in length. PriMux is a software package for selecting multiplex compatible, degenerate primers and probes to detect diverse targets such as viruses. It requires no multiple sequence alignment, instead applying k-mer algorithms, hence it scales well for large target sets and saves user effort from curating sequences into alignable groups.
Scans automatically target DNA sequences and designs primers in regions of low degeneracy that are free of secondary structures (hairpins, dimers and false priming sites). Primer Premier searches for optimal polymerase chain reaction (PCR), multiplex and single nucleotide polymorphism (SNP) genotyping primers via a nearest neighbor algorithm. It supports multiplex assays and can automatically describe BLAST search results.
Allows to design degenerate primers. GeneFisher2 is a web-based program that helps user to find primers for degenerated sequences. The software incorporates BatCons2 which allows to calculate ambiguous consensus sequence and Back-translation of amino-acid to nucleic-acid-sequences. The software provides four functions: Consensus Backtranslation, Codon Table Backtranslation, DNA and Primer Calculation.
Fast, automated and user-friendly tool to design polymerase chain reaction (PCR) primers.
A package to design degenerate primers for PCR. FAS-DPD is very strict in the search of conserved regions and minimizes the amount of degeneracy incorporated at this end. The software is designed to use multiple alignments of proteins or nucleic acids and constructs a consensus degenerate sequence from that, which is then used to design the putative primers. This tool allows a more efficient search for enzymes and other proteins with commercial or biotechnological importance, making for a faster and cheaper research process.
A command line utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.
Processes automated computational finishing and annotation of de novo viral assemblies. V-FAT can order and merge contigs, adjust frameshifts and produce NCBI-ready annotation files by using reference and read data. This software performs also several quality assurance measurements like coverage computation by amplicon or gene and identification of potential consensus errors.
Designs PCR (Polymerase Chain Reaction) primers from protein multiple-sequence alignments. CODEHOP is suited for cases where the protein sequences are distant from each other and degenerate primers are needed. Isolation of members of a rapidly evolving family of novel cytosine methyltransferase homologs from diverse plants demonstrated his practical utility.
A program for designing pairs of degenerate primers for a given set of DNA sequences. We report on the success of the program in an experimental scheme for identifying all human olfactory receptor (OR) genes. In that project, HYDEN was used to design primers with degeneracies up to 10(10) that amplified with high specificity many novel genes of that family, tripling the number of OR genes known at the time.
It was designed to predict primers for PCR amplification of homologous gene from related or diverse plant species.
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