motifs
Repeating Motif Saver 1.2.2
Repeating Motif Saver is designed as an interesting screen saver which shows repeating motif generated automatically. more>> <<less
Repeating Motif Wonderland - Repeating Motif Saver - screensaver that shows random repeating motifs. RepeatingRepeating Motif Viewer 1.1
Repeating Motif Viewer - open files which were created by Repeating Motif Saver more>> <<less
NovemberKou - Repeating Motif Generator - draw a repeating motifAmora System Icons 1.0
Amora System Icons - a complete set of system icons more>>
Ive also always like the whole black and white robot motif, so its couldnt be helped but to make a set of icons with all that material as a jumping off point.
For the most part, Ive taken my own direction with the icons, but many of them are heavily inspired by the music video, but the best way to learn is by watching the masters :)
Included in the set is a full system replacement as well as many applications, Im sure Ive missed a lot of them, but theres always time for add-ons!
I hope that you enjoy the set!
MacVector 11.0.3
MacVector offers you the ability of using a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, more>>
MacVector 11.0.3 offers you the ability of use program available for sequence analysis.
Major Features:
- Graphical Sequence Editing: MacVector can read and write DNA and Protein sequences in most popular file formats. In addition to directly editing sequences and features/annotations, MacVector has an intuitive "Click Cloning" graphical interface that lets you easily replicate laboratory cloning experiments to create new molecules.
- Gateway and Topo Cloning: MacVector supports the populay Gateway, TOPO TA and Zero Blunt cloning technologies from Invitrogen. With a few simple clicks from an intuitive graphical interface, you can replicate your biological manipulations at the bench to create new molecules with the correct sequences across the cloning and recombination junctions.
- Auto Annotation: You can scan an unannotated or partially annotated sequence against a folder on your hard drive and MacVector will identify matching features in sequences in the target folder and add them to your sequence.
- Primer Design: You can design primers for either PCR or Sequencing/Hybridization probes use in experiments.
- DNA Analysis: MacVector provides a wide variety of using "Dot-Plot" analysis and scanned for Proteolytic cleavage sites and amino acid sequence motifs. A comprehensive Protein Analysis Toolbox provides a wide variety of algorithms for analyzing the composition of proteins and presenting the results in graphical and tabular formats.
- Database Searching: MacVector has built-in Internet connectivity to the NCBI BLAST and Entrez databases. You can directly search Entrez for DNA or Protein sequences based on features, authors, keywords etc and directly download them into MacVector, complete with all features and annotations. The built-in BLAST interface lets you submit multiple BLAST jobs using a FastA algorithm, allowing for "local" database searches.
- Multiple Sequence Alignment: You can align unlimited numbers of DNA or Protein sequences ustalW algorithm built in to MacVector. A full-featured editor lets you make manual adjusing a wide variety of cused for two different functions, Sequence Confirmation and cDNA Alignment. This is included with MacVector and allows you to import trace files or sequence files and assemble them against a template sequence. This is ideal for small scale sequencing projects, especially resequencing.
Enhancements:
- Supports Gateway and TOPO cloning.
- Gateway and TOPO Cloning Support
- Auto Annotation.
- Click Cloning Enhancements
- Floating Analysis Toolbar.
- Sequence Editor Changes
- Next Generation Sequencing
- Miscellaneo
- Mac OS X 10.4 or above.
- Recommend the
- Mac OS X 10.4 or later. MacVector runs natively on both PowerPC and Intel-based Macintosh machines.
- Mac OS X 10.4 or above.
and scanned for Proteolytic cleavage sites and amino acid sequence motifs. A comprehensive Protein Analysis Toolbox provides a wide variety of algorithms for analyzing the composition of proteinsLicense:update/patch
License:update/patch
Amino Acid Motif Searches: MacVector can search for Amino Acid subsequences using a very similar approach to the Proteolytic Enzyme searching functionality. However, you can use subsequencesLicense:update/patch
CLC Protein Workbench 5.1
Advanced protein sequence anayses. more>>
CLC Protein Workbench 5.1 is a useful tool which provides a wide range of advanced protein analyses, and is based on the same user-friendly and integrated software environment as CLC Free Workbench.
This 2 x 2 weeks of fully functional demo includes a vast amount of advanced protein sequence analyses - all analyses are integrated in one single user-friendly and intuitive software application.
Major Features:
- Protein sequence analysis
- Integrated 3D molecule view
- Transmembrane helix prediction
- Antigenicity
- Secondary protein structure prediction
- PFAM domain search
- Web-based prediction of signal peptides and their cleavage sites
- Hydrophobicity analyses and graphs
- Protein charge analysis and graphs
- Reverse translation from protein to gene (a number of translation tables)
- Interactive translations of DNA and RNA to protein (both single sequences and alignments)
- Proteolytic cleavage detection
- Report of protein statistics (one or more proteins in each report)
- Comprehensive report including a range of protein analyses in one document
- 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
- 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
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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:
- Better feedback on processes: there is a tool tip showing details and start time.
- Translation of DNA to protein in sequence views can now be set to follow existing CDS/ORF annotations.
- Much improved memory performance and processing time of large data sets
- Output and error log files are now placed in the application data directory in the user home
- Fixed error when parsing files from Clone Manager (cm5-files)
- UniProt search works again
Requirements:
- 3D viewing requires an OpenGL 3D graphics driver (included with almost all graphics cards)
- Mac OS X 10.4 or later (including Intel-based Macs)
- Windows 2000, Windows XP, or Windows Vista
- Linux: Redhat or SuSE
- 256 MB RAM required
- 2 GB RAM recommended
- 1024 x 768 display recommended
Signal Peptide Prediction (SignalP) - Transmembrane helix prediction (TMHMM) - Motif search (known patterns) - Motif search using regular expressions - Motif search using ProSite patternswxWidgets 2.8.9
Free, open source and cross-platform GUI library more>> Free, open source and cross-platform GUI library
wxWidgets lets developers create applications for Win32, Mac OS X, GTK+, X11, Motif, WinCE, and more using one codebase.
wxWidgets can be used from languages such as C++, C#/.NET, Python, and Perl. Unlike other cross-platform toolkits, wxWidgets applications look and feel native.
This is because wxWidgets uses the platforms own native controls rather than emulating them. Its also extensive, free, open-source, and mature.
wxWidgets gives you a single, easy-to-use API for writing GUI applications on multiple platforms that still utilize the native platforms controls and utilities.
Link with the appropriate library for your platform (Windows/Unix/Mac, others coming shortly) and compiler (almost any popular C++ compiler), and your application will adopt the look and feel appropriate to that platform.
On top of great GUI functionality, wxWidgets gives you: online help, network programming, streams, clipboard and drag and drop, multithreading, image loading and saving in a variety of popular formats, database support, HTML viewing and printing, and much much more.
NOTE: wxWidgets is licensed under the terms of the wxWindows Library Licence.
Atari800MacX 4.2.0
Atari800MacX brings users the convenience of an Atari 800, 800XL, 130XE and 5200 emulator for Unix, Amiga, MS-DOS, Atari TT/Falcon, SDL and WinCE. more>>
Atari800MacX 4.2.0 brings users the convenience of an Atari 800, 800XL, 130XE and 5200 emulator for Unix, Amiga, MS-DOS, Atari TT/Falcon, SDL and WinCE. Our main objective is to create a freely distributable portable emulator (i.e. with source code available). It can be configured to run in the following ways :
- BASIC mode
- CURSES mode
- SVGALIB for Linux Systems
- X Window + Optional XVIEW or MOTIF User Interface
- CBM Amiga
- MS-DOS
- TOS (Atari Falcon030/TT030 and compatible)
- MS Windows (DirectX)
- SDL (many different platforms and systems)
- WinCE
- MacOS X
Enhancements:
- Added a Graphical Debugger. For a full list of debugger features see the manual or built in help. Bugs Fixed:
- Fixed issue with Cmd-key menu shortcuts when using International keyboard mapping.
- Reverted to Atari800 CVS code for PRO disk image handling, as it handles some images mine would not.
DDD for Mac OS X 3.3.9
DDD for Mac OS X is a beneficial and easy-to-use graphical front-end for command-line debuggers such as GDB, the Perl debugger, or the Python debugger. more>>
DDD for Mac OS X 3.3.9 is a beneficial and easy-to-use graphical front-end for command-line debuggers such as GDB, the Perl debugger, or the Python debugger.
Besides "usual" front-end features such as viewing source texts, DDD has become famous through its interactive graphical data display, where data structures are displayed as graphs.
- New features and minor improvements
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- Support for PHP debugger has been added. This is essentially not tested.
- Source files in subdirectories should be located automatically when using dbx (tested on Solaris dbx).
- The perl version supported by DDD is now 5.8.x. The perl debugger changed between perl 5.6.x and perl 5.8.0, which made this update necessary. This change is not backwards-compatible. If it is not possible to upgrade your perl version to 5.8.x or newer, then you can simply install the file "perl5db.pl" from a recent perl distribution into your old perl tree.
- Through the maintenance menu ("ddd --maintenance"), it now possible to get a leak check of ddd if ddd is run under valgrind. This is only useful for ddd developers (or anybody that wants to help making ddd better).
- Several minor bugs fixed, some memory leaks plugged, more code clean-up done.
- A bug affecting platforms where the size of function pointers is 16 has been fixed.
- The settings window now starts at a larger, more reasonable size, and allows the user to resize it.
- Build fixes
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- The configure machinery has been updated to conform more closely to the autoconf 2.5x requirements. Several bugs have been fixed.
- libiberty (which provides missing standard functions) is not linked by default anymore. configure has a new option --with-libiberty that enables the libiberty support if required. If nobody complains, libiberty will be unbundled in a next version.
- The libiberty distributed with ddd has been upgraded to the one included in GCC 3.4 20040116. It fixes some configuration problems.
- Builds with GCC 3.4, with IBM xlC on AIX, with Compaq/HP cxx on Tru64, on X11R5 based systems, with SGI CC on IRIX should be OK.
- Builds on HP-UX should now work out-of-the-box. Motif is linked statically and the Athena libraries are now found by default.
- Builds without Motif/Lesstif available abort with an adequate message.
- Builds with readline support now work. readline is not bundled anymore.
- Builds without -DNDEBUG (i.e. with "assert" enabled) now work. Default build enables assertions (i.e. -DNDEBUG is not used).
- Several missing files in the distribution are now included.
- Cygwin is supported again.
Ch Standard Edition 6.1
Ch Standard Edition is considered as an embeddable C/C++ interpreter designed for cross-platform scripting, shell programming, 2D/3D plotting, numerical computing, and embedded scripting. more>>
Ch Standard Edition 6.1 is considered as an embeddable C/C++ interpreter designed for cross-platform scripting, shell programming, 2D/3D plotting, numerical computing, and embedded scripting.
It is the most complete C interpreter in existence for scripting, plotting and numerical computing. It supports 1990 ISO C Standard (C90), major features in C99, classes in C++, POSIX, X11/Motif, OpenGL, ODBC, XML, GTK+, Win32, CGI, 2D/3D graphical plotting, socket/Winsock, C LAPACK, high level numeric functions, and shell programming.
Major Features:
- A complete C interpreter supporting all features in the ISO C90 Standard.
- Easy interface with C/C++ binary libraries using Ch SDK
- Wide characters in Addendum 1 for C90.
- Ch supports more new features added in the latest ISO C99 Standard than most existing C compilers. Ch is the first implementation of complex numbers, variable length arrays (VLAs), IEEE-754 floating-point arithmetic, generic mathematical functions in C99.
- Many salient C++ features including classes, objects and encapsulation for object-based programming (Brain-damaging features are excluded).
- Complex IEEE floating-point arithmetic with complex metanumbers ComplexInf and ComplexNaN.
- Assumed-shape arrays for passing multi-dimensional arrays of different sizes to the same argument of a function.
- Nested functions and nested classes for modular programming.
- Interactive execution of C statements, perfect solution for classroom demos using a laptop.
- Interactive portable shell across different platforms.
- A very-high level language (VHLL) environment for shell programming to automate tasks and system administration.
- Safe Ch with built-in secure sandbox and Ch applet for world-wide distributed network computing. As a very high-level language at the source level, a Ch applet can be very small, but with very powerful capabilities. It is especially suitable for bandwidth sensitive devices such as handheld computers and cellular phones.
- Built-in string type with automatic memory management and advanced text processing capabilities for shell programming and script computing.
- Adjustable array bounds, i.e., int a[1:10].
- Auto array bound checking.
- TCP/IP socket/WinSock for network computing.
- POSIX for portable scripting.
- Cross platform Unix utilities and commands such as vi, ls, awk, sed, mv,rm, cp, find, grep, vim with syntax highlighting for Ch, etc.
- A large number of Integrated Development Environment (IDE) support Ch. For example, ChSciTE allows you to edit, parse, and run C, Ch and C++ code within the IDE with the user interface in over 30 local languages such as German, Chinese, and Korea.
- OpenGL toolkit
- GTK+ toolkit
- Windows toolkit on Windows
- X/Motif toolkit on Unix/Linux
- Common Gateway Interface (CGI)
- Open Database Connectivity (ODBC)
- An increasing number of third party products and user contributed code
- fixed the crash for a return statement not in a function definition.
- fixed the crash for integer mod by zero intvalue%0.
Requirements:
- Mac OS X 10.3 or above
- Disk space: 69Mb
RMG QuickLook Plug-in 1.0
RMG QuickLook Plug-in provides users with a convenient plugin which helps you QuickLook the Repeating Motif Generator Document file. more>>
RMG QuickLook Plug-in 1.0 provides users with a convenient plugin which helps you QuickLook the Repeating Motif Generator Document file.
Requirements: Mac OS X 10.5
CLC Main Workbench 5.0.2
CLC Main Workbench offers you a professional and highly-efficient math and science program. more>>
CLC Main Workbench 5.0.2 offers you a professional and highly-efficient math and science program. This 4-week fully functional demo of CLC Combined Workbench aggregates all DNA sequence analysis of CLC Gene Workbench and all protein sequence analysis of CLC Protein Workbench. All analysis are fully integrated in one single, user-friendly, and intuitive software application. Some analysis are:
- Assembly of DNA sequencing data
- Advanced primer design
- Molecular cloning
- Fully integrated 1D DNA Gel Simulator
- Automatic SNP annotation of sequences
- Secondary protein structure prediction
- Integrated 3D molecular view
- Signal Peptide Prediction (SignalP)
- Transmembrane helix prediction (TMHMM)
- Protein family analysis (PFAM)
- 2 types of alignments
- Phylogenetics
- Motif search (known patterns)
- Motif search using regular expressions
- Motif search using ProSite patterns
- Pattern discovery (unknown patterns)
- Web based BLAST
- BLAST on local databases
- 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
Tony Lownds Python 2.5b1
Tony Lownds Python - Interpreted, interactive, object-oriented programming language more>>
Python combines remarkable power with very clear syntax. It has modules, classes, exceptions, very high level dynamic data types, and dynamic typing. There are interfaces to many system calls and libraries, as well as to various windowing systems (X11, Motif, Tk, Mac, MFC).
New built-in modules are easily written in C or C++. Python is also usable as an extension language for applications that need a programmable interface.
The Python implementation is portable: it runs on many brands of UNIX, on Windows, DOS, OS/2, Mac, Amiga... If your favorite system isnt listed here, it may still be supported, if theres a C compiler for it. Ask around on comp.lang.python -- or just try compiling Python yourself.
Python 3.1.1
Python is a multi-purpose, highly customizable programming language. It is often compared to Tcl, Perl, Scheme or Java. more>>
Python 3.1.1 is a multi-purpose, highly customizable programming language. It is often compared to Tcl, Perl, Scheme or Java. Python combines remarkable power with very clear syntax. It has modules, classes, exceptions, very high level dynamic data types, and dynamic typing. There are interfaces to many system calls and libraries, as well as to various windowing systems (X11, Motif, Tk, Mac, MFC). New built-in modules are easily written in C or C++.
Python is also usable as an extension language for applications that need a programmable interface.The Python implementation is portable: it runs on many brands of UNIX, on Windows, DOS, OS/2, Mac, Amiga... If your favorite system isn't listed here, it may still be supported, if there's a C compiler for it. Ask around on comp.lang.python -- or just try compiling Python yourself.
jPREdictor 1.2.3
A free and versatile tool for the prediction of cis-regulatory elements jPREdictor is used for defining motifs, searching them on sequences, weighting motifs using training sets and scoring sequences more>> A free and versatile tool for the prediction of cis-regulatory elements
jPREdictor is used for defining motifs, searching them on sequences, weighting motifs using training sets and scoring sequences using the weighted motifs.
Short sequence fragments, namely transcription factor binding sites, are known to be enriched and clustered in such elements. These binding sites are represented as motifs and for the prediction, they must be known.
Using these motifs, it is possible to weight them by applying a positive or negative training set (model or background, respectively), to search them on sequences, and to score a sequence.
Gene regulation is the process through which an organism effects spatial and temporal differences in gene expression levels. Knowledge of cis-regulatory elements as key players in gene regulation is indispensable for the understanding of the latter and of the development of organisms.
The prediction is based on clusters of individual motifs and arbitrary combinations of these into multi-motifs with selectable minimal and maximal distances. Individual motifs can be of heterogenous classes, such as simple sequence motifs or position-specific scoring matrices.
Cluster scores are weighted occurences of multi-motifs, where the weights are derived from positive and negative training sets.
System requirements:
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Enhancements
- added the new parameter searchDirection for MultiMotifs defined via option files
- fixed an error with flat triple- and higher-order motifs reporting to few hits; this error occured rarely but regulary and did not occur for DoubleMotifs or non-flat composite-motifs consising of Double- motifs, such as (Pho-DSP1)-(Pho-DSP1)
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