The Nucleic Acid Nomenclature widget displays general information on nucleic acids (symbol, meaning, complement and origin of designation) conformed with the IUPAC-IUB recommandations.

This widget is free for all users. Download it now !
Whats New in This Release:

· Inosine (I) and uracil (U) were added in the table.
· Internet links to useful information were added for adenine, cytosine, guanine, thymine, uracil, inosine, purine, pyrimidine and nucleotides.

The Amino Acid Table widget displays general information on amino acids (name, 3-letter code, 1-letter code, triplet and standard color code) conformed with the IUPAC-IUB recommendations.

Whats New in This Release:

· New information on molecular weight, composition, polarity, hydrophobicity, pK and pI for amino acids.


This widget is free for all users. Download it now !

The DNA Molar Converter widget is a Dashboard widget that allows to perform molar conversions for nucleic acids according to size.

Whats New in This Release:

· You can now perform conversions from the nucleic acid size field.

The Basic melting temperature widget allows to calculate the melting temperature of a nucleic acid sequence.

This widget is free for all users. Download it now !

The VecScreen widget provides a quick access to the system at NCBI for quickly identifying segments of a nucleic acid sequence that may be of vector origin.

You just have to type or paste your nucleic acid sequence and the result will be displayed in a new browser window.

If you ́re using Safari, click the download link. When the widget download is complete, show Dashboard, click the Plus sign to display the Widget Bar and click the widget ́s icon in the Widget Bar to open it.
If you ́re using a browser other than Safari, click the download link. When the widget download is complete, unarchive it and place it in /Library/Widgets/ in your home folder. Show Dashboard, click the Plus sign to display the Widget Bar and click the widget ́s icon in the Widget Bar to open it.

3DNA is a versatile package for analyzing and rebuilding three-dimensional nucleic acid structures, based on a standard reference frame.

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.

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry.

Jmol was originally intended to be a fully functional replacement for XMol which was a molecular viewing program developed at the Minnesota Supercomputer Center.

Although the program executables were distributed, the source code was not available to users, and since the program has not been maintained, the free binary versions have become obsolete.
Here are some key features of "Jmol":

· true 3D graphics engine that requires no special hardware
· 24 bit color with accurate lighting and shading
· substantially higher rendering performance
· handles large macromolecules with excellent performance
· protein/nucleic acid secondary structure graphics
· RasMol/Chime script compatibility.

Primer Premier is a comprehensive primer design tool with multiple features.

Design high amplification efficiency primers for PCR, sequencing and hybridization. Design cross species and pathogen detection primers in highly conserved regions using integrated multiple sequence alignment.

Here are some key features of "Primer Premier":

· PCR primer design- design primer pairs for PCR and multiplex experiments.
· Cross species- Amplify sequences from multiple species.
· Pathogenic detection- Locate oligos in highly conserved regions.
· Allele specific- Exclusively amplify a single member of a set of related sequences.
· Degenerate- Start with an amino acid sequence, reverse translate and design oligos in regions of low degeneracy automatically.
· Nested/multiplex- Checking homology among multiple candidate oligos.
· Restriction enzyme and motif analysis- Select from the database of over 800 enzymes and 200 common motifs.
· Clustal W alignments- Load the aligned sequences after performing ClustalW alignment using any resource, including EBI.
· Multiple sequence alignment- Use the popular Clustal W algorithm to align sequences from your desktop (available in Windows version only).
· Algorithm- Calculates Tm using Breslauer values.
· Long PCR- Handles sequences up to 50 KB.


Limitations:

· Registration screen at startup.

ORF Finder widget provides a quick access to the graphical tool at NCBI which finds all open reading frames in your sequence.

You just have to type or paste your nucleic acid sequence and the result will be displayed in a new browser window.

If you ́re using Safari, click the download link. When the widget download is complete, show Dashboard, click the Plus sign to display the Widget Bar and click the widget ́s icon in the Widget Bar to open it.
If you ́re using a browser other than Safari, click the download link. When the widget download is complete, unarchive it and place it in /Library/Widgets/ in your home folder. Show Dashboard, click the Plus sign to display the Widget Bar and click the widget ́s icon in the Widget Bar to open it.

CCP4MG is a protein and nucleic acid structure viewer.

Here are some key features of "CCP4MG":

· load multiple molecules (from PDB or mmCIF files) and display as cylinders, ball and stick, spheres, ribbons, worms and surfaces
· Extensive options to select and colour molecules
· calculate hydrogen bonds, close contacts, secondary structure and solvent accessible area
· displays molecule surfaces and electrostatic potential
· displays results of QM field calculations
· generate symmetry mates
· superpose structures
· load maps from MTZ, display as continuous crystal and fast changing contour level
· flexible labelling and annotation, display of images and arbitrary labelled vectors
· save image as png,jpeg etc. also PostScript or POV-Ray input file
· easy to make animated GIF or mpeg movies
· create/edit/replay scripts.

biOpen® is a new and unique nucleic acid and protein sequence analysis and structure visualization software based on dynamic integration of analysis tools.

Extensive modularity gives the user the freedom to pick the analysis tools that meet his needs and budget.

All selected tools work in a fully integrated environment with powerful display and project management capabilities.

Here are some key features of "blOpen":

· Extensive modularity: biOpen allows you to select the analysis tools you need and to work in a fully integrated environment.
· Easy evolution of your configuration: you can get new tools and integrate them in your biOpen configuration when needed.
· 3D visualization: the relations between the sequence and its structure can be studied with one single software: simply select a part of the sequence and see it light up on the structure.
· Powerful display features: fully synchronized views, dynamic display of analysis results, automated extraction and display of annotations of GenBank sequence files, and even more.
· Project management: organize and save your sequences, structures and results very easily. Import most popular file formats, including DNA Strider. Projects can be exchanged with your work colleagues.
· Graphical export: biOpen views can be simply exported in your favorite word processor or presentation software. You just have to perform a selection and drag and drop it to your document.

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. The system has several external analysis functions included for such things as automated alignment, searching, homology recognition, and phylogenetic analysis.

Whats New in This Release:

Changes to MacGDE:
· "Protections" shortcut key changed from to because of conflicts with some users setup.
· "GenBank Submission" under the "File" menu now generates a degapped FastA file with only the short name after the > and no extra data, which was not useful for submissions anyway.
· Changed the default location GDEs "Open" and "Import" commands temp files from /usr/tmp to /tmp. This was to allow the default location to be the same on all UNIX, Linux and MacOS systems. Therefore, the creation of the /usr/tmp folder on Mac OS X is no longer required.
· "Make Mega, POY or SimPlot File" under the Phylogeny 2 menu can make any of these three formats required by their respective programs. SimPlot uses FastA, where POY uses a modified FastA (no > and a return between sequences) and Mega uses its own format (# instead of >, and #MEGA as a first line with !Title "Filename" ; as the second line). This command makes all three formats with their specifics now, NOT just a FastA file to be modified by hand.

Changes to Accessory Programs:
· Added Inverted color output to MView, so the base letter is white and the background is colored.
· Added Phyml 2.4.5 under the Phylogeny 2 menu.
· Updated Blast to 2.2.14 which is now Universal.
· All parts of MacGDE are now Universal.

Sparky is a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers.

Sparky displays processed NMR spectra. You pick, assign, and integrate peaks using a graphical interface. You can work with any number of 2, 3 or 4 dimensional spectra simultaneously.

The program has been developped to assist in structure determination of proteins, DNA and RNA. Spectra for input to Sparky can be produced with processing programs NMRPipe, Felix, VNMR, XWinNMR or UXNMR.

Output consists of text peak lists showing assignments, chemical shifts, volumes, linewidths, .... Output suitable for structure determination with DYANA or XPLOR, or distance restraint calculation with MARDIGRAS can be generated.

Whats New in This Release:

· Packaged Mac version as a Mac application with an icon that can be placed on desktop or in dock.
· Still requires X windows.

Beacon Designer is a tool designed to help you design successful SYBR Green, TaqMan, LNA spiked TaqMan, molecular beacon for both standard and NASBA assays and FRET assays by interpreting BLAST results for specificity and locating oligos avoiding template structures.

Here are some key features of "Beacon Designer":

· SYBR Green Primer Design- Highly specific primers are designed by avoiding significant homologies found by automatically interpreting BLAST search results. Primer efficiency is enhanced by avoiding template secondary structures identified by connecting to the Mfold server.
· Dual Labelled Probe Design: Dual-labeled fluorescent TaqMan, molecular beacon or FRET probes can be designed with the help of Beacon Designer. For these assays, you can design new primers and probes or find probes compatible with previously designed SYBR Green assays and save on synthesis costs.
· TaqMan probes and Molecular Beacon Multiplex experiments- Multiplex assays are designed by avoiding homologies with all primers and probes in the pool. This prevents competition in multiplex real time PCR reactions and assures high signal strength.
· Allelic Discrimination- Design both wild and mutant probes for SNP genotyping assays.
· LNA Probe Design- In addition to standard TaqMan probes, Beacon Designer also designs the increasingly popular LNA or Locked Nucleic Acid substituted TaqMan probes to improve real-time PCR assay success.
· NASBA Assays- Beacon Designer designs molecular beacon probes for NASBA assays for single template, multiplex or alleleic discrimination.
· BLAST Search- Both primers and templates/amplicons can be BLAST searched against genomic databases available at NCBI or against local custom databases. This function helps verify the primer specificity.
· Avoid Template Structures- Automatically avoid secondary structures in the template identified by connecting to the Mfold server while designing primers.
· Generate Report- Generate an attractively formatted report for the assays designed. It should be helpful in record keeping and for sharing information with colleagues.


Limitations:

· The demo version is a fully functional product, except that it allows you to work only with the sequences supplied with the product.

XDrawChem is a two-dimensional molecule drawing program for Unix operating systems.

It is similar in functionality to other molecule drawing programs such as ChemDraw.

It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS

Here are some key features of "XDrawChem":

· Fixed length, fixed angle drawing.
· Automatic alignment of figures. Detects structures, text, and arrows and places them automatically.
· Can automatically draw rings and other structures - has all standard amino acids and nucleic acids in built-in library.
· Can retrieve structures from a network database based on CAS number, formula, or name. The data file (30 Mar 2005, comma-separated) is freely available.
· Can draw symbols such as partial charge, radicals, etc.
· Can read MDL Molfiles, CML [Chemical Markup Language, defined in J. Chem. Inf. Comput. Sci.39(1999), 928-942], ChemDraw(TM) binary format, ChemDraw(TM) XML text format.
· Can write MDL Molfiles, CML, ChemDraw(TM) XML text format.
· Can also read and write any format supported by the current release of OpenBabel.
· Can export pictures in PNG, Windows bitmap (*.bmp), Encapsulated PostScript (EPS), and Scalable Vector Graphics (SVG).
· Can generate 3-D structures with the help of the external program BUILD3D.
· Online help, including tool tips.
· 13C-NMR prediction, based on Bremser W, Mag. Res. Chem.23(4):271-275
· 1H-NMR prediction, based on additive rules and functional group lookup methods, described in Pretsch, Clerc, Seibl, Simon, "Tables of Spectral Data for Structure Determination of Organic Compounds", 2ed., 1989, Springer-Verlag
· Simple IR prediction.
· Simple pKa estimation.
· Octanol-water partition coefficient estimation.
· Reaction analysis: gas-phase enthalpy change estimate, 1H NMR and 13C NMR comparison.
· Integration with OpenBabel, allowing XDrawChem to read and write over 20 different chemical file formats.


Whats New in This Release:

· Worked on bug #1236716 and #1255229, regarding XDrawChems rendering of text typed into the QTextEdit mini text editor.
· Fixed bug #1254917, relating to segfaults when drawing symbols.
· Updated database back-end to use data parsed from the
· PubChem Compounds database, and updated XDrawChem to link to PubChem compound records where available.

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running Mac OS X, UNIX, or Windows, is distributed free of charge, and includes source code.

VMD is a molecular graphics program designed for the interactive visualization and analysis of biopolymers such as proteins, nucleic acids, lipids, and membranes.

VMD is a general application for displaying molecules containing any number of atoms and is similar to other molecular visualization programs in its basic capabilities.

VMD includes built-in support for high-end quad-buffered stereoscopic rendering which can be used in projection theatres as well as desktop graphics workstations. Sterescopic display aids significantly in the perception of three dimensional structures and has been a key feature in VMD since its first release. VMD also provides support for inexpensive game-oriented stereo glasses, and even anaglyphic (Red/Blue) stereo.

Whats New in This Release:

· This is the first version ported to Mac OS X on Intel x86 processors, Linux on Intel Itanium processors, and AIX 5.x on 32-bit and 64-bit POWER processors.
· Structure building, modeling, simulation setup, and analysis tasks are made easier with the introduction of the new plugins, which automate common modeling tasks.
· This release has core enhancements including support for selecting and displaying files containing multiple conformations, improved atomic mass and radius guessing, and improved handling of non-biological structures containing hundreds of thousands of atoms.

Gene Inspector, currently available for Mac OS 10.2 or later, is a unique combination of a versatile electronic laboratory research notebook and a comprehensive sequence analysis product.

Using GI, the user has the ability to define an entire suite of analyses that can be performed each time they (or anyone in the lab) has a new sequence, and the user can design custom "style sheets" which specify exactly how the output will look.

This information can then be saved as a new menu item with a name - such as "Researchers Suite #1". This feature alone will add an amazing amount of consistency within the lab - when comparing analysis results of different sequences by different researchers in the lab.

GI has one of the most versatile multiple sequence display tools available. There are over 640 different ways to display multiple sequence alignments to highlight exactly what the user wants to demonstrate. It is amazingly flexible.

Drag & Drop allows users to not only drag sequences and analysis results within Gene Inspector, but it allows objects to be dragged directly to other Drag & Drop enabled applications such as Adobe Photoshop and Illustrator, and Microsoft PowerPoint -- where they can be modified.

Because GI is an electronic notebook (in addition to performing comprehensive sequence analyses) analysis output results can have wrap-around text noting the researchers annotated thoughts and comments - together in one place. Using GI, a biologist can make use of GI Notebook Extensions that contain formatted table templates, analyses, graphics or text that he/she uses often... Each can be instantly available with the click of the mouse button.

The researcher can also use "conditional text" that can be shown or hidden - ideal for hiding notes when the researcher wants to make a poster directly from their GI Notebook. Of course in an electronic notebook, the user has access to electronic book marks and appendices. GI is quite unique.

Here are some key features of "Gene Inspector":

· Gene Inspector was designed from ground up to work the way you naturally work as a biologist you are not constrained by the structure of the program to perform tasks in a predefined way.
· Gene Inspector is centered around a powerful notebook that serves not only as a container for analysis output but as a genuine laboratory notebook and illustration tool. The Gene Inspector Notebook can contain information or annotations that you previously kept in your old fashioned paper notebook along with all your sequence analysis and laboratory experimental results. Why keep these two parts of your research artificially separated when you can combine them in a single location?
· Gene Inspector has built in hotlinking, which allows you to connect a sequence to a set of analysis routines. Each time the sequence is changed, the output results can be set to be automatically updated.
· All analyses run in background so you can continue to work in your notebook or even in other programs without interrupting the progress of the analysis.
· Gene Inspector contains analysis suites, which provide a way to create a collection of analysis routines and associated parameters that meet your needs.
· Analysis suites can be recalled by selecting them from a menu and specifying a sequence (or several sequences) to be analyzed. This provides consistency and allows even beginners to produce results that can be compared directly with those of more experienced users in the group.
· Gene Inspector contains interactive analysis output objects that allow you to fine tune analysis results to examine exactly what you are interested in.
· Gene Inspector Notebook sheets can be adjusted to any size great for designing posters, slides, or just making the notebook fit your screen - text automatically reformats to fit the notebook size.
· Gene Inspector Notebook appendices can store commonly needed information (like buffers, vector descriptions, etc.) which can be viewed at any time from any location in the notebook.
· Gene Inspector provides over 60 different nucleic acid and protein analyses including: sequence alignment, base composition/distribution, ORF determination and evaluation, restriction mapping, sophisticated multipartite find, dot matrix comparisons, antigenicity, hydropathy, transmembrane helices, helical wheel, Prosite motif searching, physical characteristics, signal sequence, protein structure prediction, and many more.
· Many analyses can be done using median sieving to bring out structures of a specific size (i.e. - membrane spanning)
· Gene Inspector allows you to easily navigate in the notebook through electronic bookmarks and aliases.
· Gene Inspector Notebook extension are instantly available with the click of your mouse button and can contain formatted table templates, analyses, graphics or text that you use often.


Limitations:

· Printing, saving, exporting disabled in Demo.

Whats New in This Release:

· Fixed a problem that sometimes lead to difficulties in opening older notebooks containing very large sequence analyses
· Increased stability when working with large notebooks
· Fixed a problem that did not allow window size to be changed in dot matrix analyses.

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

Whats New in This Release:

· 2005-07 Many bugfixes,
· graph/spectra module,
· PHYLIP interface,
· Mac OSX version.

Motion Detect is an iMovie plug-in that highlights motion in your clips. It does this by comparing to successive frames, and high-lighting differences between those frames.

Motion Detect plug has additional controls in order to amplify changes, and to suppress very small changes. It can also super-impose the original frame over the changes.

This is a highly specialized plug-in, originally developed for the scientific crowd , but the resulting effect looks nice (if strange) for the rest of us. use it whenever

you need a cool-looking moving outline
need to highlight changes (e.g. in time-compressed clips)

Here are some key features of "Motion Detect":

area of effect
· the contents of this rectangle will be affected by the plug. to resize the rectangle, click and drag into the handles. to move it, click and drag inside the rectangle.
select all
· clicking this button will select the whole surface of the clip. in the context of this plug this will mean that the clip will not be changed.
sensitivity
· this slider controls how sensitive the motion detector will be. changes below this threshold will be ignored. this is very useful if you want to suppress a background that is in constant slight motion (leaves on a tree, water flowing, steam rising, etc.)
amplify
· since the motion detector shows motion by their difference to the previous change, small changes become very dim. you can choose to amplify changes. the resulting picture may become grainy though amplification. amplification is a post-processor that only works on changes that have been detected. therefore, you don t have to adjust sensitivity after you have changed aplification.
combine
· you can choose to have the result super-imposed on the original clip. usually, parts of the clip that don t contain motion are black, while motion is high-lit according to the rate of change. if you combine this with the original clip, those parts of the clip that have motion become brighter.
frame interval
· sometimes you have original footage that was shot at a different fps than that of DV (which iMovie puts at 30 fps). upon conversion to iMovie, additional identical frames will be inserted. this will seriously impede the motion detector, since added frames do not show any motion. to avoid this, you can set the frame interval. if you set it to 1 (default), the plug assumes that every frame is unique. if your clip consists of pairs of identical frames (because it was shot at 15 fps), use 2. this plug supports footage that contains up to 5 identical frames (was shot at 6 fps).

CIDTracker is a Macintosh Caller ID program that can display Caller ID information from a compatible modem or receive Caller ID information from a compatible Caller ID server program such as another copy of CIDTracker or CallerID Sentry for Windows, ACID Server for the 3COM Ergo Audrey Internet Appliance or YAC.

Here are some key features of "CIDTracker":

· Can decode Caller ID information from a modem attached to your Macintosh. (i.e. can act as a CID Server)
· Can receive Caller ID information from CIDTracker operating in server mode or CallerID Sentry or ACID Server (when they are acting as CID servers) or YAC.
· Shows list of received call and can log the information to a text file.
· Can run an AppleScript when call comes in.
· Can send an E-Mail when call comes in.


Limitations:

· 30 days trial.