Software



Service @ BC

ncbi Blast Local BLAST server at BBSC. We offer the service of builting and maintaining customized databases for the labs at IMB.


Supported Software:

-Custom Software Utilities by BBSC

GCV Genome Comparison Viewer is a software utility that allows users to visualize differences among closely related viral genomes at both the gene level and the sequence level.
CUE The tool gives a visual overview of the relative codon frequencies of the given DNA sequence compared to the selected host (reference) organism.

-Commercial Softwares available to IMB labs

vectorNTI VectorNTI - a user-friendly software for biologists.

Tutorials:

  1. Construction - Insert a fragment into Vector(Chinese) (Download)
  2. Vector NTI Tutorial(English) (Download)
  3. ocumentation and Tutorials(English) (Download)
  4. How to import sequences into VectorNTI(Example)
    -Gnepept Format Batch import

Vector NTI Advance 9.1(Nov.15,2004)

  1. Vector NTI 9.1(Download) (XP,Me,2000,98 SE,or NT 4.0 SP6)
  2. Quick Start Guide for Vector NTI Advance 9.1(English) (Download)
  3. User Manual of VNTI 9.1(English) (Download)
  4. Installation Guide(English) (Download)
  5. Invitrogen Vectors Data Set (Download)
  6. User Manual of VNTI 7.1(Chinese) (Download)

Tutorials:

  • Importing Two-Channel Raw Expression Data(Part I) (Download)
  • Adding Annotations to Imported Two-Channel Raw Expression Data(Part II) (Download)
  • Creating a Script for Automating Normalization of Two-Channel Data(Part III) (Download)
GeneSpring GX10 provides powerful, accessible statistical tools for fast visualization and analysis of expression data. Designed specifically for the needs of biologists, GeneSpring GX10 offers an interactive desktop computing environment that promotes investigation and enables understanding of microarray data within a biological context.

GX10 Software Donload:
Here is the example.(Screen 2 Needed)
CLC logo CLC MainWorkbench 5.2 trial to 2009/12/31

CLC Website:
Download the CLC Program for
During you install the CLC Program, you also need these:
CLC know how
  • Biological Sequence Analy...LC Main Workbench(Chinese version) (Download)
  • Biological Sequence Analy... Using CLC Main Workbench(Powerpoint) (Download)
MacVector11 MacVector12 is 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, and a variety of other functions. MacVector is widely regarded as the most intuitive, easy to use program available for sequence analysis.

MacVector12 Software:


Tutorials:



Free Open Source Software

-For Windows Users

pymol PyMOL is a USER-SPONSORED molecular modeling system with an OPEN-SOURCE foundation.
Swiss PDB viewer Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
VMD VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

-For Linux Users

CNSsolve Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination.
CCP4 logo The CCP4 program suite is a collection of disparate programs covering most of the computations required for macromolecular crystallography.
EMBOSS EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.

-For Unix(IRIX) Users

Alscript Alscript is a program to format multiple sequence alignments in PostScript for publication and to assist in analysis. Alscript does not support point-and-click, but has a scripting language to allow compex effects.
Catalyst CatalystR provides an integrated environment for database management and querying tasks that are extremely valuable in drug discovery research. This integrated environment allows for seamless access to complementary capabilities such as pharmacophore-based alignment of molecules, shape-based three-dimensional searching, automated generation of pharmacophore hypotheses based on SAR data, and generation of multiple conformations with extensive coverage of conformational space.
CCP4 logo The CCP4 program suite is a collection of disparate programs covering most of the computations required for macromolecular crystallography.
Cerius2 Cerius2 provides an easy-to-use simulation and modeling environment, offering a broad range of scientific application modules. Select the modules that are relevent to your research to create a customized and integrated package.
grasp logo GRASP is a molecular visualization and analysis program. It is particularly useful for the display and manipulation of the surfaces of molecules and their electrostatic properties.
modeller logo MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms.
Molscript 2.1.2 MolScript is a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
Raster3D logo Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing.
TOP diplay TOP is a protein TOPlogical comparision program. It can detect wether there are toplogical similiarities between two protein structures. If you have a new protein structure, the program can be used for searching if there are similar structures in the PROTEIN DATA BANK. The program can also be used for automatic comparision without previous knowledge about which residues are corressponding each other in the two structures.