| COMAP 1.0a
|
MS-DOS |
| COMAP is a graphically orientated program for helping with the construction of restriction maps of small DNA fragments from digestion data. |
|
|
Download (540 kb, 15-Mar-1993) |
|
| 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: CONFAC
|
|
|
| CPL: Collection Programming Language
|
Internet Browser |
| The goal of the CPL project is to provide a uniform query interface to heterogeneous biological data sources. |
|
Web Site: University of Pennsylvania
|
|
|
| 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: DNA Baser - Free biology software
|
|
|
| Cleaner
|
Internet Browser |
| With this tool you can simply and quickly clean your sequences from unwanted text marks and spaces. This is useful after retrieving sequences from online databases for example. |
|
Web Site: JustBio.com
|
|
|
| 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: CodonCode Aligner Sequence Assembly and Alignment
|
|
|
| Codons 1.4
|
MS-DOS |
| Program for analysing codon usage of a target DNA sequence. |
|
|
Download (65 kb, 28-Jul-1992) |
|
| Codontree
|
MS-DOS Unix Windows |
| This program is able to determine a codon usage table for a set of protein coding genes, gene relationship on the basis of codon usage similarity, and compositional features of protein coding genes. |
|
Web Site: National Research Council Bari
|
|
|
| Complementor
|
Internet Browser |
| With this tool you can quickly get the complementary (reversed or not) of your DNA sequence. |
|
Web Site: JustBio.com
|
|
|
| ConsInspector 3.0 (Windows)
|
Windows |
| The program ConsInspector predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. For Windows 95/98/NT. |
|
Web Site: AG BIODV
|
Download (3351 kb, 01-Aug-1996) |
|
| ConsInspector 3.3 (Alpha)
|
Unix |
| The program ConsInspector predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. For DEC Alpha (Digital Unix 4.0). |
|
Web Site: AG BIODV
|
Download (343 kb, 01-Mar-1998) |
|
| ConsInspector 3.3 (HP)
|
Unix |
| The program ConsInspector predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. For HP (HP-UX 10.2). |
|
Web Site: AG BIODV
|
Download (369 kb, 01-Mar-1998) |
|
| ConsInspector 3.3 (Irix)
|
Unix |
| The program ConsInspector predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. For SGI (IRIX 6.2). |
|
Web Site: AG BIODV
|
Download (340 kb, 01-Mar-1998) |
|
| ConsInspector 3.3 (Linux)
|
Unix |
| The program ConsInspector predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. For PC x86 (Linux 2.0). |
|
Web Site: AG BIODV
|
Download (291 kb, 01-Mar-1998) |
|
| ConsInspector 3.3 (Sun)
|
Unix |
| The program ConsInspector predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. For SUN (SunOS 5.5). |
|
Web Site: AG BIODV
|
Download (340 kb, 01-Mar-1998) |
|
| ConsInspector 3.3 Installation Notes
|
Unix |
| Installation notes for Unix versions of ConsInspector. The program ConsInspector predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. |
|
Web Site: AG BIODV
|
Download (3 kb, 01-Mar-1998) |
|
| Consinspector 3.0 (Mac)
|
Mac |
| The program ConsInspector predicts potential binding sites in sequences of unlimited length by comparing candidates with predefined consensus descriptions of protein binding sites. |
|
Web Site: AG BIODV
|
Download (686 kb, 01-May-1998) |
|
| Coresearch
|
Unix |
| This program is used to identify and delimitate consensus elements (e.g. protein binding sites) in a set of unaligned nucleic acid sequences. |
|
Web Site: AG BIODV
|
|
|
| CounterTrace II DNA sequencing system
|
Linux Unix Windows |
The CounterTrace II DNA sequencing system offers a novel way of increasing automated sequencing read lengths by up to 30%. The CounterTrace II system is comprised of a proprietary DNA sizing reagent added post sample clean up and a Windows-based trace processing software package. The CounterTrace reagent is a DNA fragments ladder labeled with a broad wavelength fluorescent dye. The CounterTrace II software uses the location of the CounterTrace reagent peaks within each trace file to enable better processing of the raw channel data. The resulting improved automated DNA traces are suitable for base- and quality-calling using the ABI KB basecaller. CounterTrace II is designed for use with the ABI3730 and 3730xl DNA sequencing instruments. In high-throughput DNA sequencing facilities, users can expect average read length increases of 15–20%. A version of the CounterTrace II sequencing software suitable for use in DNA sequencing core facilities is also available. |
|
Web Site: Nucleics DNA sequencing software
|
|
|
| CpG
|
Internet Browser |
| CpG islands prediction. |
|
Web Site: WebGene
|
|
|
| CpG Islands
|
Internet Browser |
| Utility to find CpG Islands in a user-entered sequence. |
|
Web Site: EBI
|
|
|
| Cutter
|
Internet Browser |
| With this tool you can quickly get the list of all enzyme restriction sites on your sequence. |
|
Web Site: JustBio.com
|
|
|
| DFA
|
Unix |
| The DFA (deterministic finite-state automata) library for use in building the BLAST application programs for biosequence similarity searching. |
|
|
Download (80 kb, 15-Jun-1992) |
|
| DIG - Analysis, Reporting, Intelligence
|
Linux Unix Windows |
| DIG is a Data Analysis, Reporting, Intelligence tool for data workers, labs, and webmasters. Use DIG to clean up duplicates, consolidate, trim, query, summarize large data set in Excel/Access, log files, Oracle, MySQL, lab or POS systems, or any databases. Comes with powerful Excel/Access add-ons, ad-hoc query & multi-dimensional analysis. Watch on-line demo, get a free 30-day trial, then pay $96/yr or $8/month. |
|
Web Site: DigDB
|
|
|
| DNA Baser - an affordable alternative to the really expensive software on the market
|
Mac Windows |
| DNA Baser has been designed as a tool for fast assembly of DNA sequences. We had in mind a fast assembly engine and implementation of a number of features that greatly reduce the required user input. These features (see the Features page) have been successfully implemented, so that the current version of DNA Baser can assemble 4 trace files with about 800 nucleotides each within 2 seconds on an average system configuration. End trimming of the original trace files, suggestions for correction of ambiguous bases based on quality values, automatic removal of cloning vector sequences from the final contig are only some examples of fully functional features that makes the assembly of DNA sequences much easier and less time-consuming. Some of the alignment core features are: * Very fast assembly algorithm: the assembly of four SCF files with 800 nucleotides each takes less than 3 seconds on an average computer (AMD/INTEL 1.2 GHz) * It will automatically clean (trim) the ends of o chromatogram if the Quality Values (QV) is very poor. The resolution of the trimming engine can be fully adjusted by the user; this operation saves significant time, as manual ‘cleaning’ of the trace sequences is not needed any more. * The original trace files and the generated contig are synchronized and displayed as such, making the correction of ambiguous bases much easier * Using the QV, DNA Baser makes suggestions for correction of the ambiguous bases; the rate of correct suggestions recorded during testing was more than 95%. This means that the user must only confirm the software’s suggestions, which again decreases the overall processing time * Reverse-complement: reverse sequences are automatically turned during assembly * Automatic cut of vector/primer sequence. Create your own primer database by adding your primers. Using this database, DNA Baser will remove the primer from the final contig * Viewing of trace files (format ABI and SCF) Special features * BEST price on the market and significant discount when several licenses are ordered. Please see the Prices page for more details * Intelligent, ergonomic, easy to use interface. Just drag and drop your files, then press the |
|
Web Site: DNA Baser - DNA assembly tool
|
|
|
