| Sequence Analysis for Mac OS X
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Mac |
| 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 for Macintosh OS X in order to promote the platform and to encourage migration from Classic. |
 Web Site: Sequence Analysis for Mac OS X
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| Sequence Space
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Unix Windows |
| Sequence Space is a method of clustering aligned protein sequences. The algorithm developed by Casari, Sander and Valencia converts each sequence in the input multiple alignment into a single vector in a high dimensional "Sequence Space". 2- or 3-dimensional viewing of the resulting clusters is possible with Java viewers. |
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Web Site: EBI
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| Serial Cloner
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Mac Windows |
| Version 1.3 - Serial Cloner is a Molecular Biology software that provides tools with an intuitive interface to assists you in DNA cloning, sequence analysis and visualization. Serial Cloner can read and write DNA Strider-compatible files and also import or export files in FASTA format (or in pDRAW32 format). Powerful graphical display tools and simple interfaces help the analysis and construction steps in a very intuitive way. All the tools you need to analyze and manipulate your sequences are available in an all-in-one-window concept. Numerically select fragments, find restriction sites, ORF or any motif, calculate Tm of selected fragments, %GC or dynamically determine the translation your selection into peptide and calculate the MW using a compact interface. Serial Cloner also lets you build text restriction map and quickly format it to add multi-frame translation or only show single cutters for example. The graphic map of Serial Cloner is really Graphic as you can easily select and extract a fragment or show single, double or multiple cutter all in the same window. Serial Cloner will assist you in setting-up new sub-cloning projects and in preparing the electronic versions of your constructs. In addition to the classical restriction maps - both graphic and text-based - or site usage windows, you will be able to quickly extract a sub-sequence either in a selection or between restriction sites, to create a new PCR-based fragment or synthetic adaptors. shRNA constructions based on pre-defined scaffolds are also automated. You can assemble fragments, obtained by PCR, adaptor/shRNA synthesis or simply by graphically selecting fragments between restriction sites. Just select, blunt if you need, and click the Ligate button. An additional interface allows easy Gateway(tm) cloning for both BP and LR reactions. Finally, Serial Cloner provides an interface to align two sequences using a local algorithm or the BLAST2Seq NCBI server and extract a consensus. Version 1.3 now adds a virtual cutter, a web browser with instant import of NCBI/EMBL entries and a silent restriction map together with other enhancements. Addition/Correction in version 1.3 - [New]: Virtual Cutter Window with simulated gel migration . - [New]: Small Web browser with instant parsing of NCBI/EMBL entries. - [New]: A silent map window has been added to see what site could be introduced in a sequence without changing the translation. - [Updated]: A consensus sequence can be extracted after a local alignment. - [Updated]: Print character size can be set independently of screen character size - [Updated] : Peptides can be numerically selected in the “information” window. - [Updated] : The DNA sequence corresponding to the selected peptide can be “back” selected. - [Updated] : Point mutation can be added when preparing a shRNA construct. - [Addition] : ORF can be found and translated in both strands. - [Addition]: Alternative start codons can be selected for translation. - [Addition] : Direct selection of PCR primers in the Sequence window. - [Fixed] : several bugs and interface fixes in particular under windows (toolbar glitch, behavior when reduced in the Taskbar, etc.). |
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Web Site: Serial Cloner HomePage
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| ShadyBox 1.1
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Unix |
| ShadyBox is a drawing program which enables you to box and shade regular and irregular shaped segments of aligned multiple sequences. It was designed with the intention of producing PostScript output suitable for use in publications. |
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Web Site: University of Sydney
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Download (4324 kb, 01-Jun-1994) |
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| Spectrum
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Mac Windows |
| A program designed to read in a data file comprising aligned character arrays (such as DNA sequence data) or distance data in the form of a matrix, and perform some simple spectral analysis procedures on that data. |
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Web Site: Taxonomy and Systematics, University of Glasgow
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| TDAlign 1.61
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MS-DOS |
| Sequence alignment program. |
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Download (85 kb, 18-Nov-1989) |
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| Three
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Mac |
| Aligns three protein sequences up to 1000 amino acids in length. |
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Download (70 kb, 29-Sep-1989) |
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| ToPLign
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Internet Browser |
| ToPLign implements standard pairwise and multiple alignment methods with flexible parameter handling. The analysis of alignments is supported by offering different visualisations of alignments. In addition, ToPLign includes innovative approaches to the parametric alignment problem and the threading problem. |
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Web Site: GMD (German National Research Center for Information Technology)
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| Unipro UGENE
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Linux Mac Unix Windows |
| UGENE is a free software aimed to integrate most of the important molecular biology tools within a single graphical environment. UGENE can be run on Linux, Windows and MacOS platforms and is tuned to utilize resources of modern multi-core and GPU hardware. |
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Web Site: Unipro UGENE - Integrated Bioinformatics Tools
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| aminoXpress
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Internet Browser Windows |
| More than 12 aminoXpress ActiveX Controls integrated with such functions as Amino Acid Analysis, Building Block Sort, Digestion, Elemental Analysis, Mass Fragmentation, HPLC Retention Pattern, Isotopic Profile, Combinatorial Library, Molecular Weight, Sequence Parameters, Charge-pH Profile, ... ... |
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Web Site: aminoXpress Platform
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| mrtrans
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Unix |
| mrtrans is a simple program that allows you to produce aligned cDNA sequences from aligned protein sequences. This can be very useful for phylogeny programs, e.g. in PHYLIP \- dnadist, dnapars, dnaml, etc. |
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Download (9 kb, 24-Jun-1993) |
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| pir39b Protein Sequence Database
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MS-DOS Mac Unix VMS |
| Protein sequence database used in evaluation of sequence comparison programs. |
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Download (3167 kb, 24-Dec-1995) |
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| sp34 Protein Sequence Database
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Unix |
| Protein sequence database used in evaluation of sequence comparison programs. |
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Download (13725 kb, 01-Jan-1998) |
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| strap
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Linux Mac Unix Windows |
| The computer program STRAP supports the analysis of proteins and protein alignments. It integrates amino acid sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence and residue annotation. Several included tutorials will teach the use of modern bioinformatics software within the integrated STRAP environment. The scriptability and extendability make STRAP a very powerful tool for even the most advanced users. The STRAP software is programmed in JAVA and the free scripting API is available at http://strapjava.de. For 3D visualisation either Pymol or Jmol can be used. |
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Web Site: STRAP workbench for protein sequences and structures
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