Pcr Primer Design
Primer Design is a simple utility created in order to design DNA primers for mutagenesis in the BGME lab (JHU).
It allows users to select or enter background sequence and add current and new mutations. During the design process, users are presented with various updating checks to guide them.
Platforms: Windows
License: Freeware | Download (477): Primer Design Download |
This is the high throughput PCR primer design software that is used at the J. Craig Venter Institute. See: Li K, et al. 'Novel computational methods for increasing PCR primer design effectiveness in directed sequencing'. BMC Bioinformatics 2008, 9:191.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 181.36 MB | Download (49): JCVI Primer Designer Download |
RAPD Primer Design from Metagenomes (RPD-M) scans metagenome sequences identifying and determining relative frequency of candidate primers for Random Amplification of Polymorphic DNA (RAPD) assays.
Platforms: Mac, BSD, Linux
License: Freeware | Size: 15.61 KB | Download (45): RAPD Primer Design from Metagenomes Download |
ORFer reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. ORFprimer is an extended software package for high throughput PCR primer design for biological sequences
Platforms: Windows, Mac, BSD, Solaris, Linux
License: Freeware | Size: 240.93 KB | Download (47): ORFprimer - primer design for ORFs Download |
The FastPCR software was developed to be an integrated tools environment that provides comprehensive facilities for designing primers for most PCR applications including standard, long distance, inverse, real-time, multiplex, unique and group-specific; overlap extension PCR (OE-PCR)...
Platforms: Windows, XP, 2003, Windows Vista, XPX64, 7, 7x64
License: Freeware | Download (466): FastPCR Professional Download |
Bio::MCPrimers is a Perl module to create molecular cloning PCR primer pairs for a given gene so that the gene can be directionally inserted into a vector. Solver is generic, restriction enzymes and their order in the vector are specified in the caller. XPORT SUBROUTINES sub find_mc_primers...
Platforms: *nix
License: Freeware | Size: 174.08 KB | Download (109): Bio::MCPrimers Download |
Design primers based on length, melting temperature, GC content, hairpins, dimerization, nucleotide repeats, and 3' GC clamp criteria.Import data from files or from Genbank.
Platforms: Matlab
License: Shareware | Cost: $0.00 USD | Size: 20.48 KB | Download (43): Primer Design GUI Download |
BioAssistant was written to improve on Probe Assistant, CSL's first attempt at a tool to assist PCR Chemists design DNA Probes. With BioAssistant you can do all the things you could do with Probe Assistant, such as determine probe Melting Points, Molecular Weights, Hybridization information and...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 662 KB | Download (98): BioAssistant Download |
AlleleID is a comprehensive desktop tool designed to address the challenges of pathogen detection, bacterial identification or taxa/species discrimination using microarrays and TaqMan® and molecular beacon qPCR assays. With ClustalW multiple sequence alignment at its core, AlleleID can design...
Platforms: Mac
License: Demo | Cost: $0.00 USD | Download (124): AlleleID Download |
IMP is an automated tool for intron-flanking primer design based off of Expressed Sequence Tags (ESTs). It's intended for use in species with limited to no genomic sequence data available.
Platforms: Mac, BSD, Linux
License: Freeware | Size: 197.35 KB | Download (47): intron marker pipeline Download |
A GUI program to create the plasmid database forms for BGME lab. This program presents user with a data entry form for entering plasmid information and automatically converts DNA sequence to protein, aligns it, and creates text output file.
Platforms: Mac
License: Freeware | Size: 40.96 KB | Download (48): Primer Design Tool Download |
OLIGO is a multi-functional program that searches for and selects oligonucleotides from a sequence file for polymerase chain reaction (PCR), DNA sequencing, site-directed mutagenesis, and various hybridization applications. It calculates hybridization temperature and secondary structure of...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Download (169): Oligo Download |
PerlPrimer is a free, open-source GUI application written in Perl that designs primers for standard PCR, bisulphite PCR, real-time PCR (QPCR) and sequencing. It aims to automate and simplify the process of primer design.PerlPrimer's current features include the following: - Calculation of...
Platforms: *nix, Perl, BSD
License: Freeware | Download (58): PerlPrimer Download |
msatcommander is a python program written to locate microsatellite (SSR, VNTR, &c) repeats within fasta-formatted sequence or consensus files. msatcommander will search for all di-, tri-, tetra-, penta-, and hexa-nucleotide repeats (with options to search for fewer repeat types and combinations...
Platforms: Mac
License: Freeware | Size: 11.7 MB | Download (279): msatcommander Download |
MethMarker facilitates the design and optimization of gene-specific DNA methylation assays. Beyond its use as an epigenetic primer-design tool, it provides extensive support for epigenetic biomarker optimization. For a given gene or genomic region, MethMarker helps design DNA methylation assays...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 30.72 KB | Download (51): MethMarker Download |
MacVector... Researchers who want a simple but comprehensive desktop sequence analysis application continually turn to MacVector, the leading sequence analysis package for the Macintosh. MacVector provides sequence editing, primer design, Internet database searches, protein analysis, sequence...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Download (126): MacVector Download |
UGENE is a free cross-platform genome analysis suite. It works perfectly on Windows, Mac OS or Linux and requires only a few clicks to install. Features: * Multiple sequence alignment using MUSCLE 3, KAlign, Clustal; * HMM profiles build and search, based on the source of HMMER 2 and HMMER...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 30.7 MB | Download (35): Unipro UGENE Download |
Sequence Analysis project is a collage of coding projects which I have written over the past several years for various clients in my work as a bioinformatics consultant. These clients have graciously allowed me to release these works into the public domain as freeware for Macintosh OS X in...
Platforms: *nix
License: Freeware | Size: 2.3 MB | Download (122): Sequence Analysis Download |
CLC DNA Workbench (formerly known as CLC Gene Workbench) creates a software environment enabling users to make a large number of advanced DNA sequence analyses, combined with smooth data management, and excellent graphical viewing and output options.We invite you to try a fully functional demo of...
Platforms: Mac
License: Demo | Cost: $0.00 USD | Download (94): CLC DNA Workbench Download |
Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis,...
Platforms: Windows
License: Shareware | Cost: $249.00 USD | Size: 30 MB | Download (433): Geneious PRO Download |