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Integrated Bioinformatics Software

  • GCG
GCG is one of the earliest integrated bioinformatics system. It maintains more than 70 bioinformatics data analysis tools, which are based on published algorithms from fields of mathematical and computational biology. In additions to running these programs individually, GCG allows the data flow among them. By using these tools, scientists can accomplish the following tasks:

  Sequence Comparison
  Database Searching and Retrieval
  DNA/RNA Secondary Structure Prediction
  Editing and Publication
  Evolution Analysis
  Fragment Assembly
  Gene Finding and Pattern Recognition
  Importing and Exporting Files in Different Formats
  Primer Selection
  Protein Analysis

  • BioTools (GeneTool & PepTool)
BioTools Suite includes GeneTool and PepTool for nucleotide and peptide sequence analysis respectively. Compared to GCG and Vector NTI, BioTools has the most user-friendly interface. It covers almost all routine bioinformatics jobs while the analysis function is less powerful than GCG and Vector NTI. However, we find BioTools is a very good software for bioinformatics novices and basic analysis. It's much better developed and more reliable than those freeware you can get from the Internet. Here we list some features of BioTools.

  Chromatogram Analysis and Sequence Assembly
  Database Reference Search and BLAST Search
  Multiple Alignment
  Vector Construct
  Primer Design
  Biochemistry Statistics of Nucleotide & Protein Sequence
  Restriction Map

  • BioEdit
In addition to a sequence alignment editor, BioEdit is also connected with a wide range of free bioinformatics programs on the Internet. The topics cover from BLAST search to promoter prediction. If you want to get some freeware, BioEdit is a good one you may want to have a look at.

  • PDRAW32
PDRAW32 produces good graphical displays for sequence annotation, restriction map and gel simulation, in addition to some other analysis functions, such as primer design and similarity search. It's a good freeware to do in silicon cloning.

  • Wingene
WinGene is an application for Win95/Win98/Win NT for analysis of nucleotide sequences. For analysis of polypeptide sequences,

  Possible Actions
  Reverse complement a given sequence.
  Translate the sequence in all reading frames and identify ORFs.
  Export polypeptides encoded by a given ORF into WinPep.
  Perform a oligomer analysis (base composition and melting temperature).
  Perform a restriction analysis.

  • Tinker
The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L), Liam Dang's polarizable potentials, and our own AMOEBA polarizable atomic multipole force field. Parameter sets for other standard force fields such as GROMOS, UFF, ENCAD and MM4 are under consideration for future releases