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ABI to FASTA free converter Windows
This free tool will batch convert all (selected) ABI files to FASTA files. All you need to do is to locate your ABI chromatogram files and press the CONVERT button. With this automatic converter you can convert hundreds or thousands of ABI chromatogram files in seconds. All with A SINGLE PUSH OF A BUTTON! ---------- No installation process is required.
Web Site Home Web Site: DNA Baser Contig Assembler

AiO Windows
Software package combining DNA/protein programs with oligonucleotide Data Base management. It is written multi-user and multi-group. However, it can be run on a single PC for single user. Features: DNA-editor, DNA with restriction enzymes, DNA with oligos, PCR tables, plasmid maps, linear maps, dotplot, alignments, ORF finding, translate, backtranslate, flow (virtual cloning), editors for data banks (oligos, structural DNA etc), online oligo ordering..........
Web Site Home Web Site: AiO - All in One - AiO

AlleleID 4 Mac  Windows
AlleleID supports real time PCR primer design, design of TaqMan, SYBR Green primer design, TaqMan MGB probe design and design of microarrays for detecting gene splicing and alternative splicing. AlleleID can be used to design cross species assays, assays for bacterial identification, species identification and strain detection. You can align the nucleotide sequences to locate differences in DNA and to find unique or conserved regions and then design oligos to amplify and detect either species or strains of interest from the mix. AlleleID also supports assays for selectively amplifying cDNA from gDNA.
Web Site Home Web Site: PREMIER Biosoft

AlleleID 5
AlleleID designs real time PCR and microarray probes and primers for identifying strains and sequences from an alignment and for amplifying and detecting patterns across sequences. AlleleID has a built-in ClustalW alignment module which aligns the nucleotide sequences. You can choose to amplify and detect sequence specific or conserved regions from the mix. AlleleID supports TaqMan, molecular beacons, Fret, TaqMan MGB and Microarray probes. A distinguishing feature of AlleleID is the ability to design real time PCR primers and probes to spot and amplify exons/introns
Web Site Home Web Site: Premier Biosoft

AlleleID version 6 Mac  Windows
AlleleID the comprehensive primer design tool can now design mutation specific/mRNA specific or DNA specific MLPA probes that are compatible with Pamchip array.
Web Site Home Web Site: Premier Biosoft

Amplify 1.2 Mac
Tool for checking PCR primers.
Web Site Home Web Site: University of Wisconsin, Genetics Download  (200 kb, 02-Jun-1993)

ApE Linux  Mac  Unix  Windows
ApE is designed to be an all-in-one molecular biology workbench. It can read strider, EMBL, genbank, Fasta sequence file formats. In addition it can read and display ABI trace files. It can query and download from the NCBI EMBL database and can blast sequences directly at the NCBI BLAST server. Sequence features can be added individually or automatically from pre-defined feature definition libraries. It can draw graphic (liear or circular) and text-based restriction maps that include annotated features of the sequence. It contains a restriction enzyme choser that can perform boolean queries for enzymes that match cut frequency and enzyme property parameters. It can show virtual agarose gels. It can align two sequences or a sequence and an ABI trace file. It can search selected sequence for potential PCR primers matching given parameters. All analysis functions are hyperlinked back to the original sequence. Other features of the program are listed on the website.
Web Site Home Web Site: ApE- A plasmid Editor

Array Designer Linux  Mac
Array Designer is a high-throughput program for designing highly specific oligos for expression and SNP detection microarrays. The program has a unique homology avoidance algorithm that ensures high specificity. The sequences are BLASTed, the results are automatically interpreted and the most optimal oligos are designed avoiding regions of signinficant homology. The program enables BLAST search of the oligos designed. This feature helps in verifying their specificity. It is also possible to BLAST search sequences against all the databases available at NCBI for cross species studies. The design can be exported in a convenient spreadsheet format for ordering synthesis.conditions.
Web Site Home Web Site: PREMIER Biosoft International

Array Designer 4 Linux  Windows
Array Designer designs highly efficient, specific oligos for SNP genotyping, and expression microarrays. You can start with a list of sequences or the whole genome sequence in standard format to study entire organisms effortlessly. Using a sophisticated algorithm, the program automatically interprets BLAST results and designs highly specific oligos. The oligos and templates can then be BLAST searched against private local databases or all genomic public databases available at NCBI, including the redundant nr database to verify the specificity of the design. With Array Designer, you can even design tiling arrays to spot every base of a long genomic sequence, avoiding repetitive regions. Designing arrays to characterize regulatory elements, or to study epigenetic modifications, methylation patterns and protein binding sites has never been so easy.
Web Site Home Web Site: www.premierbiosoft.com

Beacon Designer Mac  Windows
Beacon Designer is a comprehensive real time PCR primer and probe design tool that is supported on Win amd Mac OS. Beacon Designer designs optimal SYBR® Green primers, TaqMan® probes, LNA spiked TaqMan® probes, molecular beacon for both standard and NASBA® assays, and FRET probes for real time quantitative PCR assays. Highly specific primers are designed by avoiding cross homologies found by automatically interpreting BLAST search results. Primer efficiency is enhanced by avoiding template secondary structures identified by connecting to the Mfold server. Beacon Designer can be used to evaluate predesigned assays and designing compatible oligos to extend the designs. It can design molecular beacons and TaqMan® probes for single tube multiplex experiments. Version 6 of Beacon Designer helps researchers design MethyLight assays using TaqMan probes for detecting DNA methylation and predicting CpG islands using real time PCR
Web Site Home Web Site: PREMER Biosoft International

Beacon Designer Mac  Windows
Beacon Designer is a tool for designing probes and primers for real time detection of PCR products. Designs primers and probes for multiplex and allele discrimination assays. Displays secondary structures in a simple graphical format. Uses statistical optimization techniques to output the best rated primer/probe pair. Generates a list of alternate probes to meet specific research needs. Allows complete control over design parameters. Evaluates pre-designed/published beacons and primers. Integrates to web to BLAST search and open sequences from Entrez. Exports results in a tab delimited format ready to be loaded into a database, spreadsheet, or sent for oligo synthesis.
Web Site Home Web Site: PREMIER Biosoft

Beacon Designer 2 Mac  Windows
Comprehensive tool for designing Taqman(R) and Molecular Beacon probes and PCR primer pairs for both multiplex and allele descrimination assays. Integrated BLAST search facility ensures specificity of the designed probes by avoiding cross homologies. The program helps in analysing the designed primers using programs intuitive graphical interface. You can even evaluate a predesigned primer.
Web Site Home Web Site: PREMIER Biosoft International

Beacon Designer 4 Mac  Windows
Beacon Designer is a tool for designing primers and probes for real time detection of PCR products and for multiplex and allele discrimination assays. It designs SYBR Green primers, TaqMan probes, FRET probes and molecular beacons for robust amplification and fluorescence in real time QPCR. It also evaluates pre-designed/published beacons and primers. Beacon Designer displays secondary structures in a graphical format for easy interpretation, uses statistical optimization techniques to output the best rated primer/probe pair and generates a list of alternate probes to meet specific research needs and allows complete control over design parameters.
Web Site Home Web Site: www.premierbiosoft.com

Beacon Designer Free Edition Internet Browser
Beacon Designer Free Edition is a free web based oligo properties calculator for analysing SYBR Green Primers and TaqMan Probes for possible secoondary structures such and for accurately calculating Primer and Probe Tm. Beacon Designer free edition also displays sequence details such as sequence length, runs, repeats, reverse, reverse complement and GC%.
Web Site Home Web Site: Premier Biosoft

BioNumerics Windows
One universal bioinformatics solution to store and analyze all your biological data. Powerful databasing, integrated networking and a wide range of analysis, visualization and decision-making tools, including data mining, querying, clustering, identification, statistics, and much more. With applications for bacteriology, virology and mycology including features for surveillance networks for bacterial (Salmonella, E. coli & Shigella, Campylobacter spp., Listeria monocytogenes, Vibrio cholerae, Vibrio parahaemolyticus, Yersinia pestis, etc.) and viral pathogens (norovirus).
Web Site Home Web Site: Applied Maths

BioToolKit Mac  Windows
BioToolKit is a collection of tools frequently used by bench biomedical scientists. Functions include centrifugation speed/force conversion, molecular weight calculation for chemicals, oligos, and peptides, molar concentration calculator, OD calculator, recipe calculator, clinical calculator, primer design, peptide antigen design, grade book, and label printing.
Web Site Home Web Site: Chang Bioscience

CLC Combined Workbench Linux  Mac  Windows
CLC Combined Workbench 1.0 aggregates all DNA sequence analyses of CLC Gene Workbench and all protein sequence analyses of CLC Protein Workbench. All analyses are fully integrated in one single, user-friendly, and intuitive software application. Some analyses are - Assembly of DNA sequencing data - Advanced primer design - Molecular cloning - Automatic SNP annotation of sequences - Secondary protein structure prediction - Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Protein family analysis (PFAM) - 2 types of alignments - Phylogenetics - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Dot plots - Hydrophobicity analyses - Antigenicity analyses - Searches on GenBank, SwissProt, TrEMBL, and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

CLC Gene Workbench Linux  Mac  Windows
CLC Gene Workbench 1.0 provides a wide range of advanced DNA sequence analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are - Assembly of DNA sequencing data - Advanced primer design - Molecular cloning - Automatic SNP annotation of sequences - 2 types of alignments - Phylogenetics - Motif search (known patterns) - Pattern discovery (unknown patterns) - BLAST - Batch processing of multiple analyses in one work-step - Dot plots - Hydrophobicity analyses - Searches on GenBank and PubMed - Detailed log of actions/analyses performed
Web Site Home Web Site: CLC bio

Chromatogram Explorer-Exploring and trimming your chromatograms is not a problem anymore Mac  Windows
Chromatogram Explorer is a very easy to use tool that will list all chromatogram files (SCF, ABI, AB1, AB) in the current folder. You can view the chromatograms while browsing through folders using its integrated Windows Explorer. Chromatogram Explorer can also trim low quality bases at the ends of your samples with a single push of a button! Now you can process/sort/search chromatograms in seconds.
Web Site Home Web Site: DNA Baser - Free biology software

DNA Club Windows
A DNA sequence analysis program, featuring PCR primer design, translation, complementing, orf mapping, restriction enzyme mapping. For Windows 95/98/NT. Freeware.
Download  (971 kb, 21-Oct-1998)

DNAWorks Windows
DNAWorks is a computer program that automates the design of oligonucleotides for gene synthesis. The program requires simple input information, i.e. amino acid sequence of the target protein and melting temperature (needed for the gene assembly) of synthetic oligonucleotides. The program outputs a series of oligonucleotide sequences with codons optimized for expression in an organism of choice. These oligonucleotides are characterized by highly homogeneous melting temperatures and minimized tendency for hairpin formation.
Web Site Home Web Site: Lubkowsky Jacek, Ph.D.

Electronic PCR (ePCR) Internet Browser
PCR-based sequence tagged sites (STSs) have been used as landmarks for construction of various types of genomic maps. Using
Web Site Home Web Site: NCBI

Expression Windows
Expression is a revolutionary new application for DNA and protein sequence analysis. Utilising a novel interface, Expression makes complex computational analyses of sequence information incredibly simple. Expression uses the very latest computing technology to set new standards in the way sequences are analysed. Features include: Sequence Annotation,Graphical Sequence Map, Degenerate DNA and Amino Acid Sequence Support, Restriction Analysis, Primer Design and Analysis, ORF Prediction, Pattern Finding, Reverse Translation, GenBank Searching, Pattern and Motif Identification, Multiple Sequence Alignment, and Protein Structure Prediction.
Web Site Home Web Site: Genamics

GENtle Windows
GENtle is a program for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, specialized calculators, PCR, gel image display, virtual gel simulation, and more.

GPRIME MS-DOS  Windows
This program helps with the design of PCR primers for an aligned group of related nucleotide sequences.
Web Site Home Web Site: Bioinformatics Group, Research School of Biological Sciences

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