dna
3DNA 1.5
3DNA - Analyze and rebuild 3D nucleic acid structures more>>
In its core, the software uses a simple, yet mathematically rigorous and geometrically sensible, scheme for calculating a complete set of local base-pair, step, and helical parameters, and allows for exact rebuilding of a structure based on these parameters.
Unique features of 3DNA include automatic classification of a dinucleotide step as A-, B-, or TA-like based on the positioning of the phosphorus atoms, and the generation of "standardized" base stacking diagrams. The rebuilding routines give Calladine-Drew style schematic representations of DNA as well as full atomic models with the sugar-phosphate backbone.
DNA Artist X 1.0
DNA Artist X is a program including small Molecular Biology programs. Y more>>
DNA Artist X 1.0 is a program including small Molecular Biology programs. You can do things like search for Compatible Enzyme ends or do a PCR Melting point temperature calculation with different formulas, or you can run a Digest Preview of an Agarose Gel etc.
DNA Artist is an Internet Application, which means it works like an Internet browser (e.g. Netscape Navigator or Internet Explorer).
The Application Navigator is the central access point of DNA Artist,it connects to the Internet and downloads small files, which are interpreted from the application and compiled into a form that you can actually use these modules as individual programs.
CLC DNA Workbench 5.5
CLC DNA Workbench 5.5 is a helpful program that 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. more>>
CLC DNA Workbench 5.5 is helpful program that 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. This 4-week fully functional demo of CLC Gene Workbench 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.
Major Features:
- DNA sequence analysis
- Editor for graphically and algorithmically advanced primer design
- Assembly of DNA sequence data
- Multiplexing - Process Tagged Sequences has an option to filter away groups with few sequences.
- Molecular cloning
- Automatic SNP annotation of sequences
- Local complexity region analyses
- Reverse translation from protein to gene, based on translation tables from a number of species
- Advanced restriction enzyme analysis and management
- Dot plot based analyses
- DNA statistics report including a number of characteristics of a given molecule
- NCBI sequence data search
- Access to web info from PubMed
- 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)
- Database searches
- Web-based sequence search using BLAST
- BLAST on local databases
- Build local BLAST databases
- GenBank Entrez searches
- UniProt searches (SwissProt/TrEMBL)
- PubMed lookup
- Web-based lookup in UniProt, NCBI, and Google
- SNP annotation using BLAST
- Project and data management
- Full integration of data input, data management, calculation results, and data export
- Detailed history log
- All types of files can be saved in local projects, and launched from the program
- Import and export of data in a large number of file formats
- Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects
- Other bioinformatics features
- DNA, RNA and protein sequence editor displaying both linear and circular molecules
- Multiple alignment of DNA, RNA, and proteins
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- Two proprietary algorithms
- ClustalW
- Muscle
- T-Coffee
- MAFFT
- Kalign
- Joining multiple alignments into one
- DNA, RNA, and protein alignment editor
- Interactive logo graphs along both DNA, RNA and Protein alignments
- Batch processing of analyses on multiple sequences in one work-step
- Advanced re-alignment and fix-point alignment option
- Manual annotation of sequences
- Dot plot based analyses
- Local complexity region analyses and complexity plots
- Gap fraction graphs
- G/C content analysis and graphs
- Advanced pairwise comparison
- Extract annotations
Enhancements:
- Gateway cloning. Simple and easy-to-use support for creating Gateway entry and expression clones.
- Search for matches among all your saved primers. The Find Binding Sites tool has been greatly improved to now allow you to search among all your primers. In addition, you also get a tabular output of the binding sites and possible fragments.
- In silico PCR: create PCR product based on primer pair and template sequence (including primer extensions). As part of the improve...
Requirements:
- Mac OS X 10.4 or later (including Intel-based Macs)
- Windows 2000, XP, Vista, or Windows 7
- Linux: Redhat or SuSE
- 256 MB RAM required
- 2 GB RAM recommended
- 1024 x 768 display recommended
CLC DNA Workbench is considered as a flexible program that provides a wide range of advanced DNA sequence analyses, and is based on the same user-friendlyLicense:update/patch
CLC bio A/S - Advanced DNA sequence analyses. CLC DNA WorkbenchCLC DNA Workbench is designed to be a 4-week completely powerful demo of CLC Gene Workbench which provides a wide range of advanced DNA sequence analysesDNA Molar Converter Widget 1.2
DNA Molar Converter Widget - Widget for molar coversions more>>
Enhancements:
- You can now perform conversions from the nucleic acid size field.
AbOrygen - DNA Molar Converter Widget - A great dashboard widget for molar coversions. DNA Molar ConverterLicense:Freeware
DNA/Protein Converter 1.0
DNA/Protein Converter is a widget to convert sizes between DNA and protein. more>>
DNA/Protein Converter 1.0 is a widget to convert sizes between DNA and protein.
DNA/Protein Converter Widget 1.0
The DNA/Protein Converter widget allows to perform size conversions between DNA and protein more>>
Requirements:
- Mac OS X 10.4 or later.
iRNAi 2.1
iRNAi - RNA interference remover for gene functions more>>
Nowadays, the use of so-called RNA interference is a common technique applied by molecular biologists to determine the function of the many genes in our genome.
Unfortunately, the design of oligonucleotides, the building blocks for this technique, is a time-consuming and error-prone task. iRNAi completely turns this into history, both eliminating mistakes and hours of stupidious work.
Enhancements:
- Support for additional file formats, including EnzymeX files
- Better printing support
- Improved behaviour of the sequence view.
Genomorama 1.5
Genomorama - Multi-scale, multi-genome visualization and analysis more>>
Main features:
- Fast, interactive genome visualization
- PCR primer prediction
- PCR amplicon prediction.
Enhancements:
- Added a selection guide for picking nucleotide sequence to display and translate into amino acids.
- Fixed bug that caused clipping rectange to overlap neighbooring genomes.
- Fixed bug in sequence selection (a selection that ended on the last base of the genome caused an infinite loop!).
- Added a new annotation key to the GBK file parser -- "signature".
- Fixed bug when inverting genome plot.
- Fixed bug when parsing genome files with no genomes.
- Fixed bug when clipping multiple genomes.
- No longer throw an error when the GIF color table is exhausted -- use the closest color available instead.
- Added the ability to import genome annotations from Protein Translation Table (ptt) files.
- Fixed a bug in exact match DNA searching.
- Added the ability to import annotations from any genome file that contains annotation (i.e. asn, gbk, embl, ptt). As with loading files, the file type is autodetected!
- Fixed a import bug in the GBK file format (assigning GI values)
- Added a horizontal scroll bar for scrolling all genomes left and right
- Added a vertical scroll bar for zooming all genomes
- Added the ability to export genome data (i.e. sequence and annotation) to the following formats: Fasta (protein and DNA), PTT and GBK
- Fixed line numbers on GBK parse error messages.
- Fixed lack of intergenic space for certain annotation combinations.
- Fixed bug in the translation guide rendering (that could cause infinite loop under certain conditions).
- Pressing the esc key now cancels any pending translation.
- Added the ability to load multiple genomes from a single ASN file.
- Fixed the rendering of *multiple* annotations that all overlap the origin.
- Added search by genome name.
- Modifed the EMBL parser to handle Artemis files.
- Fixed bug in searching for Padlock/MOL-PCR probes
- Added an annotation editor
Central Dogma 1.1
A small application to translate nucleotide sequences and back-translate amino acid sequences among other uses. more>>
The central dogma of biology is that a sequence of DNA nucleotides is copied to a seqeunce of mRNA nucleotides that serves as a template for protein production. The basic concept is essential for even a rudimentary knowledge of biology.
Central Dogma is meant to be a simple tool to experiment and practice this concept from a high school level and up. For instance, the effect of point mutations and frame shifts on protein sequence can be seen instantly. The statistics panel provides a way to get a quick look at the makeup of a protein.
application for biological translation and back-translation for amino acids and RNA and DNA moleculesSequence Analysis 1.6
Sequence Analysis - DNA/protein sequence analysis more>>
This (Java) application 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.
Enhancements:
- Fixed launching conflict introduced with QuickTime 7.0.4
- Digest: Using "REBase 601" enzyme list
- Allow launching with Java 5 (JDK 1.5).
CLC RNA Workbench 4.2
CLC RNA Workbench brings you an easy way to a range of complex algorithms and options. RNA secondary structures can be predicted using state-of-the-art free energy minimization algorithms. more>>
CLC RNA Workbench 4.2 brings you an easy way to a range of complex algorithms and options. RNA secondary structures can be predicted using state-of-the-art free energy minimization algorithms.
Major Benefits:
- You will have easy access to a large number of integrated research tools:
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- Secondary structure prediction
- Graphical view and editing of secondary structure
- Tabular view of structures and energy contributions
- Symbolic representation in sequence view
- You can make your computer a High Performance Computing center
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- Unleash the hidden powers in your CPU with the Bioinformatics Cell
- Plug in the Bioinformatics Cube and increase your search speed up to 200 times
- Your research work will be easy to carry out
- The program is graphically based, intuitive, and user-friendly
- Share data with your colleagues using CLC Database Solution
- You will have a bioinformatics solution that continuously evolves
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- The frequent program updates keep you up to date with the latest scientific developments. Your ideas for future improvements will have top priority.
- You can customize your workbench
- You have the possibility to customize your workbench through our Software Developer Kit.
Major Features:
- Bioinformatics features in CLC RNA Workbench
- Secondary structure prediction
- Graphical view and editing of secondary structure
- Tabular view of structures and energy contributions
- Symbolic representation 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
- Full integration of data input, data management, calculation results, and data export
- Detailed history log
- All types of files can be saved in local projects, and launched from the program
- Import and export of data in a large number of file formats
- Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects
- Other bioinformatics features
- DNA, RNA and protein sequence editor displaying both linear and circular molecules
- Multiple alignment of DNA, RNA, and proteins
-
- Two proprietary algorithms
- ClustalW
- Muscle
- T-Coffee
- MAFFT
- Kalign
- Joining multiple alignments into one
- DNA, RNA, and protein alignment editor
- Interactive logo graphs along both DNA, RNA and Protein alignments
- Batch processing of analyses on multiple sequences in one work-step
- Advanced re-alignment and fix-point alignment option
- Manual annotation of sequences
- Dot plot based analyses
- Local complexity region analyses and complexity plots
- Gap fraction graphs
- G/C content analysis and graphs
- Advanced pairwise comparison
- Extract annotations
- Database searches
- Web based sequence search using BLAST
- BLAST on local databases
- Build local BLAST databases
- GenBank Entrez searches
- PubMed lookup
- Web based lookup in UniProt, NCBI, and Google
Enhancements:
- New features:
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- Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
- Advanced view of elements in a folder including batch editing.
- Extract sequences improvements
- You can now drag results from NCBI searches into the view area to open directly (previously you could only drag into a folder to save)
- "Find" in text view now accepts Enter as command to find the next hit
- Importing VectorNTI archives previously resulted in a sequence list. Now it imports as single sequences.
- Export of annotations in GFF format (note that annotations with joined regions are not supported)
- Bug fixes:
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- Fixed tblastn numbering issue
- Problem rendering scatter plots without lines
- DNA strider files could loose name upon import
- Rare misplacement of annotations when editing very large sequences
- Various bug-fixes
DNA, RNA and protein sequence editor displaying both linear and circular molecules. Multiple alignment of DNA, RNA, and proteins. Two proprietary algorithms. ClustalW. Muscle. T-Coffee. MAFFT. KalignpythonFastaToGenbank 1
Convert protein or DNA sequences from fasta to genbank more>> Convert protein or DNA sequences from fasta to genbank
pythonFastaToGenbank is a simple Python program for converting protein or DNA sequences from Fasta to genbank. Requires Python 2.4, output in python console.
Enhancements
- Version one of the PyFastatoGen.py
- Single .py File
- PyConverter.py: A v. simple python program. Uses standard
- text editing to convert sequence data (either DNA or
- protein) from Fasta format (single line) to genbank
- format(spaced and line numbered). Basically a little bit
- of code to save some time, rather then formatting it by
- hand in a text editor. Warning: there is no checking of
- the sequence you enter, remember GIGO!
- requires python 2.4, output in python
MacGDE 2.4
A set of programs for multiple sequence alignment and analysis. MacGDE is a set of programs for multiple sequence alignment and analysis more>> A set of programs for multiple sequence alignment and analysis.
MacGDE is a set of programs for multiple sequence alignment and analysis. The programs use an expandable user interface which allows the addition of external analysis functions without any rewriting of code.
The system supports several data types, nucleic and amino acid sequences, text, and masking sequence, and three forms of color highlighting. MacGDE has several external analysis functions included for such things as homology recognition, automated alignment, searching and phylogenetic analysis.
System requirements:
- X11 Windowing environment.
Enhancements
- Fixed the window size setting so MacGDE does not open larger than the viewing screen.
- Added "GDE Full or Basic menus" under the File menu so users could have GDE without all of the additions I have made. This removes the Phylogeny menus and lots of other programs that I have added. You can switch between the two menu but you must open a new GDE window to see the changes.
- Modified the Import Foreign Format command so that only the data from the file is brought in leaving the original file alone.
- A copy of the file ending with .gde is no longer made. A WARNING is now given to remember to name the file with the Save As... command after importing.
- Import Foreign Format now recognizes Clustal format files by using clustalw (must be present) included with MacGDE.
- Added a View Chromat Sequence command to view chromatograms in LifeTrace. This uses a panel just like the Open and Import commands to locate the file and open it.
- Import Chromat and View Chromat Sequence commands now handle spaces in directory (folder) names.
- But the names of the chromat files can NOT have any spaces.
- DeSoete tree files now end in .tre so Treeview X will open them directly.
- Changed the Mr. Bayes MCMC settings for the consensus type to be "All Compatible".
- This now matches the default settings of Mr. Bayes and often adds resolution and support to nodes.
- Under PAUP the MultiCPU has been changed to 2 or 4 CPUs. Since most computers now have 2 or 4 CPUs
- I changed the run options so that the bootstraps can be run automatically. I have removed the manual option. Hopefully, this will make it easier for everyone to get their PAUP bootstraps done more quickly.
- Added an Overwrite Database feature to the Manage DNA BLAST DataBases LOCAL and Manage Protein BLAST DataBases LOCAL under the Sequence Management menu. This will let you replace an entire existing database.
- Useful if you accidentally added something to a database you did not mean to.
- This has the same effect as Deleting then recreating a database, but just in one step.
Addition of New Program:
- Parallel Mr. Bayes (Phylogeny 1 > MrBayes3.1.2 Run Options) you can choose one processor (this runs regular Mr. Bayes) or 2 or 4 processors (runs pMrBayes). You will need to be running Mac OS 10.5 or better for this to work and have 2 or 4 processors.
- PhyML 3.0 under Phylogeny 2 uses the Phylip-like interface.
- ProtTest 2.1 under Phylogeny 1
- SNAP: Synonymous Non-synonymous Analysis Program under the DNA/RNA menu. This program calculates synonymous and non-synonymous substitution rates based on a set of codon-aligned nucleotide sequences.
- Synonymous or Non-synonymous Distance Tree (SNAP) under the Phylogeny 2 menu. This uses SNAP to generate a ds or dn distance matrix that can be analyzed with the Neighbor program from the Phylip package to create trees.
Updates to Other programs:
- BLAST is now at version 2.2.20
- CAP2 (Sequence Management>Assemble Contigs) will now maintain the name of the sequences up to 50 characters.
- Phylip is now at version 3.68
EnzymeX 3.1
EnzymeX - Enzyme scientific program more>>
EnzymeX features a set of unique and powerful tools to easily help you pick the right enzyme and buffer for each reaction.
In addition, it gives you all the specific properties of these enzymes so that you can make sure that every digestion is a success.
Enhancements:
- Drastically improved speed
- Spotlight integration, including the new spotlight-based file browser
- Support for reverse ORFs
- Many improvements
- Improved accurateness
- Tons of bug fixes
- And much much more...
GENtle 1.8.5
GENtle - A multi-purpose molecular biology tool more>>
Enhancements:
- 2005-07 Many bugfixes,
- graph/spectra module,
- PHYLIP interface,
- Mac OSX version.
