About the GCG Wisconsin Package
The Wisconsin Package consists of over 130 programs that allow you to manipulate and analyze nucleic acid and protein sequences. Scientists from all over the world have collaborated to develop and refine the Wisconsin Package, making it a flexible tool with which to analyze your sequence data.
The Wisconsin Package provides three interfaces for your analysis needs:
- SeqWeb. Provides a web interface to a core set of Wisconsin Package programs.
- SeqLab. Based on X Windows, SeqLab provides a point-and-click multiple sequence editor and annotation tool with access to all Wisconsin Package programs.
- Command-Line. Each program steps you through the required parameters it needs to run. Add optional parameters to the command-line for customized analyses. Scriptable command lines provide the ability to do repetitive and numerous analyses.
Among its many features, the Wisconsin Package gives you access to the following functions:
Note As indicated below, not all functions listed are available from SeqWeb. If a function is not available in SeqWeb, you may want to try the command-line or the SeqLab interface to the Wisconsin Package.
- Editing and Publication. Enter sequences from a digitizer (available only from the command-line interface) or a keyboard and edit them.
- Fragment Assembly. Manage and assemble nucleotide sequence fragments in a sequencing project. (Available only in the command-line interface and SeqLab.)
- Mapping. Calculate and display restriction digests and simulate RNA fingerprints.
- Comparison. Compare two or more sequences. Create, edit, display, and analyze multiple sequence alignments.
- Database Searching and Retrieval. Search nucleic acid or protein sequence databases for sequences similar to your query sequence or sequence pattern.
- Evolution. Determine and display evolutionary phylogenies from multiple sequence alignments.
- Gene Finding and Pattern Recognition. Recognize terminators, repeats, protein coding regions, and other consensus patterns.
- Nucleic Acid Secondary Structure. Predict and display optimal and suboptimal DNA/RNA secondary structures.
- Protein Analysis. Identify sequence motifs in protein sequences and make predictions about peptide isolation.
- Translation. Translate nucleic acids into proteins and backtranslate proteins into nucleic acids.
- Primer Prediction. Predict optimal primers for PCR reactions.