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2D Hunt Internet Browser
2-D Electrophoresis Finder provides an interface for searching 2D electrophoresis-related pages on the web, by keyword.
Web Site Home Web Site: Expasy

ABI Trace Data, Lab and Computer Protocols: Washington U.-Merck Human EST Project Internet Browser
Users of EST data may directly view the original trace data, which is useful in interpreting sequencing results, using the 'View a Sequence' function on the home page.
Web Site Home Web Site: Washington University

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

Acedb Software (mac, Unix) Mac  Unix  Windows
ACEDB is an acronym for A Caenorhabditis elegans Database. ACEDB is being adapted by many groups to organize molecular biology data about the genomes of diverse species. ACEDB allows for automatic cross-referencing of items during loading and allows for hypertextual navigation of the links using a graphical user interface and mouse. Certain special purpose graphical displays have been integrated into the software. These reflect the needs of molecular biologists in constructing genetic and physical maps of genomes.
Web Site Home Web Site: Stanford Genomic Resources

Aligner Internet Browser
With this tool you can align easily your multiple sequences DNA or protein, based on a Clustalw engine.
Web Site Home Web Site: JustBio.com

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

Array Mapper 2 Windows
Array Mapper automates the mapping of DNA samples during a microarray printing process. It controls the array printer as well as exports the map to an imaging software, saving hours of manual calculations of sample locations. It supports preprinting for improved experimental reproducibility and single, double, or triple spot replication.
Web Site Home Web Site: PREMIER Biosoft International

Artemis Linux  Mac  Unix  Windows
Artemis is a DNA sequence viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, reads EMBL-format sequences and feature tables, and can work on sequences of any size from a few kb to entire genomes of 5 Mb or more. Written in Java.
Web Site Home Web Site: Sanger Center

BLASTView Internet Browser
Demonstration of bioWidgets toolkit for processing BLAST search results.
Web Site Home Web Site: CBIL, University of Pennsylvania

BibioSphere PathwayEdition Internet Browser  Linux  Mac  Unix  Windows
BiblioSpherePE allows for dynamic data-driven network/pathway construction and analysis based on literature, the Genomatix Knowledge Base, and promoter DNA sequence analysis. It is an important component of the micro array data analysis pipeline offered by Genomatix.
Web Site Home Web Site: Genomatix

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

CELL Suite Windows
Incellico's Cell Suite being offered as a modular portfolio of research and discovery tools that will individually, and as a whole, respond to the specific challenges faced by life sciences researchers across the spectrum of biotechnology and bioinformatics problem solving. CELL acts as a librarian of public and private databases, automatically cross-referencing entities like genes and proteins that appear in those databases, and building a searchable, ontology-based network of cross-references that reveals the relationships between entities of interest to a user.
Web Site Home Web Site: Incellico

CLC Bioinformatics Cell Linux  Mac  Windows
CLC Bioinformatics Cell is a High Performance Computing product, accelerating Smith Waterman based BLAST-searches up to 400 times and Clustal W alignments up to 20 times. It can be run command line with the same parameters as NCBI BLAST, or through the graphical user interface of CLC Gene Workbench, CLC Protein Workbench, or CLC Combined Workbench.
Web Site Home Web Site: CLC Bioinformatics Cell

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 Free Workbench 1.0 Linux  Mac  Windows
CLC Free Workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management, combined with excellent graphical viewing and output options. Some bioinformatics features are: - GenBank searching and viewing (linear and circular views) - Multiple alignment of DNA, RNA and proteins (2 alignment algorithms) - Open reading frame determination - Translation from DNA to proteins (all genetic translation tables) - Reports with residue composition, molecular weight and iso electric point (for proteins) - Neighbor-joining and UPGMA phylogenies - Restriction site analysis and viewing - Other reporting facilities - Import/export to a number of data formats - Launch of external files - Detailed History Log
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

CLC RNA Workbench Linux  Mac  Windows
CLC RNA Workbench aggregates a large number of advanced RNA sequence analyses and other bioinformatics analyses in one single, integrated, user-friendly, and intuitive software application. Some features are Secondary RNA structure prediction, Graphical view and editing of secondary RNA structures, Tabular view of RNA structures and RNA energy contributions, Symbolic representation of RNAs in sequence view, Pattern search, Search for sequence matches, Motif search for basic patterns, Motif search using regular expressions, Motif search with ProSite patterns, Pattern discovery (unknown patterns), Project and data management, Detailed history log, All types of files can be saved in local projects, and launched from the program, DNA, RNA and protein sequence editor displaying both linear and circular molecules, Multiple alignment of DNA, RNA, and proteins: ClustalW, Muscle, T-Coffee, MAFFT, Kalign. Interactive logo graphs along both DNA, RNA and Protein alignments, BLAST, and much more.
Web Site Home Web Site: www.clcbio.com

CONFAC Internet Browser
CONFAC identifies significantly enriched and evolutionarily conserved transcription factor binding sites (TFBS) quickly for sets of hundreds of genes found to be co-expressed by microarray analysis.
Web Site Home Web Site: CONFAC

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

Codon Usage Database Internet Browser
Codon usage database of various organisms.
Web Site Home Web Site: Kazusa DNA Research institute

CodonCode Aligner Sequence Assembler Mac  Windows
CodonCode Aligner is user-friendly software for DNA sequence assembly and alignment. Features include end clipping, vector trimming, sequence assembly, alignment to reference sequences, cDNA to genomic DNA alignment, contig editing, and mutation detection. CodonCode Aligner offers many time saving and unique features, including the ability to align contigs with Clustal and muscle, trace sharpening, roundtrip editing, and base calling with Phred.
Web Site Home Web Site: CodonCode Aligner Sequence Assembly and Alignment

Complementor Internet Browser
With this tool you can quickly get the complementary (reversed or not) of your DNA sequence.
Web Site Home Web Site: JustBio.com

Completed Genomes Search and Analysis Internet Browser
BLAST and keyword searches of the functional annotation of the completed genome databases. Search includes BMERC ID, as well as the Genbank PID and EMBL ID when known.
Web Site Home Web Site: BMERC, Boston University

CoreGenes Internet Browser
Identifies "core" genes from a set of two to five small genomes
Web Site Home Web Site: Bioinformatics & Computational Biology, George Mason University

CounterTrace II DNA sequencing software Linux  Windows
The CounterTrace II DNA sequencing software increases alignable KB Q20+ read lengths by up to 30%. Current state-of-the-art capillary DNA sequencers can produce reads that exceed 1000 bases. However, these long DNA sequencing reads typically suffer from excessive peak broadening and poor resolution in the later part of the trace. This latter region is associated with low quality scores and high base call error rates. CounterTrace II uses an internal calibration standard to allow the accurate measurement and processing of each sequencing trace. The CounterTrace additive contains DNA fragments of known size labeled with a proprietary fluorophore (CounterTrace standard). This fluorophore has been designed to enable its specific detection in four channel sequence data. Addition of the CounterTrace standard to each sequencing reaction after sample clean-up provides unique ‘landmark’ sizing peaks in the raw trace data. The CounterTrace II software uses the location of the standard peaks to enable accurate sizing and processing of the trace data. After algorithmic removal of the standard peaks from the trace data, the CounterTrace II software output sequencing trace file in the ab1 format. These trace file are then able to base- and quality-called using the KB DNA sequencing basecaller.
Web Site Home Web Site: Nucleics DNA sequencing reagents & software

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