Sequence Analysis Software at BimCore
Genetics Computer Group (GCG)
The GCG software package is composed of over 100 programs providing a large suite of analysis tools at the user's disposal. These programs are located on a Sun Microsystems UNIX machine running the Solaris operating system and are accessed from the users personal computer (PC or Macintosh). The package can be accessed via a command-line interface, an X windows graphical interface (SeqLab), or a web interface (SeqWeb). The GCG programs are divided into the following functional categories:
- Comparison
- Editing and Publication
- Fragment Assembly
- Importing and Exporting
- Primer Selection
- RNA Secondary Structure
- Database Searching
- Evolution
- Gene Finding and Pattern Recognition
- Mapping
- Protein Analysis
- Translation
- Utilities
| Name | Description | Download | Homepage | Manuals | Tutorial/ Examples |
|---|---|---|---|---|---|
| Genetics Computer Group (GCG) | Extensive Sequence Analysis Package SeqWeb (Web Interface) |
NA |  |
 (accessible only from emory.edu
nodes). |
NA |
LaserGene by DNASTAR
[See some BIMCORE tutorials written for DNASTAR]
[Download a demo version of DNASTAR]
| Module | Description | Homepage | Manuals | Tutorial/ Examples |
|---|---|---|---|---|
| EditSeq | Sequence Input and Editing | EditSeq homepage | NA | NA |
| MapDraw | Restriction Mapping | MapDraw homepage | NA | NA |
| GeneMan | Biological Database Browsing | DNASTAR homepage | NA | NA |
| PrimerSelect | Primer Design and Analysis | PrimerSelect homepage | NA | NA |
| SeqMan | Sequence Fragment Assembly | SeqMan homepage | NA | NA |
| GeneQuest | DNA Sequence Analysis | GeneQuest homepage | NA | NA |
| MegAlign | Multiple and Pairwise Sequence Aligment | MegAlign homepage | NA | NA |
| Protean | Protein Sequence Analysis | Protean homepage | NA | NA |
Multiple Sequence Analysis
| Name | Description | Download | Homepage | Manuals | Tutorial/ Examples |
|---|---|---|---|---|---|
| ClustalW | Multiple Sequence Alignment Program | NA | BCM Search Launcher | Clustal W manual | Clustal examples |
| Jalview | Java Multiple Alignment Editor | NA | Jalview Homepage | Jalview Manual | N/A |
| ShadyBox | Muliple Sequence Blocks and Shading | NA | ShadyBox homepage | ShadyBox manual | NA |
Pattern Recognition
| Name | Description | Download | Homepage | Manuals | Tutorial/ Examples |
|---|---|---|---|---|---|
| GeneMark | GeneFinding by Markov Models | NA | GeneMark homepage | GeneMark instructions | NA |
| TropPred | Topology Prediction | NA | NA | NA | NA |
| TransMembrane | Membrane Spanning Protein Finder | NA | NA | NA | NA |
| ProScan | ProScan | NA | ProScan homepage | NA | NA |
Miscellaneous
| Name | Description | Download | Homepage | Manuals | Tutorial/ Examples |
|---|---|---|---|---|---|
| Readseq | Reformats Biosequences | NA | Run WWW Interface for Readseq (N/A) | Readseq Help Page (N/A) | Run WWW Interface for Readseq (N/A) |
| Protein Splitter | Splits Protein Sequences into short overlapping fragments | NA | Run WWW Interface for Protein Splitter | NA | Run WWW Interface for Protein Splitter |
| Acedb | A C. elegans Data Analysis Package | Download Instructions | AceDB Home | Documen-tation | NA |
| Phred, Phrap, CrossMatch, and Consed | High Throughput Sequence Assembly | Download Instructions | Phred/ Phrap/ Consed Home | Documen-tation | NA |
| RHMAP | Radiation Hybrid Mapping | NA | RHAMP Home | RHAMP Manual | |
| Phylip | Phylogenetic Data Analysis | Download Phylip | Phylip homepage | Phylip manual | NA |
| Staden | Fragment Assembly | Staden availability | Staden homepage | Staden manual | NA |