BCCL Software

BLAST
Purpose: Sequence similarity search program

NCBI-BLAST
WU-BLAST
NR
SWISSPROT
GO
UniVec

BTAB
Purpose: BLAST output parser

CAP3
Purpose: Sequence assembly program

CLUSTALW
Purpose: Multiple sequence alignment program

DAG-EDIT
Purpose: Java application which provides an interface to browse, query and edit GO or any other vocabulary that has a DAG data structure

DIOGENES
Purpose: Program for the identification of coding region in short genomic sequences

DISPLAY MUMS
Purpose:Program which graphically presents alignments of MUMs from a set of query sequences and a single reference sequence

CONSED&AUTOFINISH
Purpose: graphical editor, automated finishing program

EMBOSS
Purpose: The European Molecular Biology Open Software Suite

FASTA
Purpose: Alignment and similarity search program

GCG Wisconsin Package
Purpose: Sequence analysis software suite

GCG Databases
Purpose: Database Collection

GenBank
EMBL (Abridged)
GenPept
PIR-PROTEIN
NRL_3D
SWISS-PROT
SP-TREMBL
PROSITE
PFAM
REBASE

GCG Seqweb
Purpose: Web interface for GCG Wisconsin Package admin account: gcgadmin

http://watson.vcu.edu
http://watson.vcu.edu/install.html

GenMAPP
Purpose: Gene Map Annotator and Pathway Profiler is a computer program designed for viewing and analyzing gene expression data on maps representing biological pathways and other groupings of genes. mplete gene structures in genomic DNA

GENSCAN
Purpose:Program for the identification of complete gene structures in genomic DNA

GENEWISE
Purpose:Comparison of DNA sequence at the level of its protein translation

GLIMMER
Purpose:Program for finding genes in microbial DNA, especially the genomes of bacteria and archaea

GLIMMERM
Purpose: A gene finder derived from Glimmer, but developed specifically for eukaryotes

GRAIL EXP
Purpose: Software package that predicts exons, genes, promoters, polyas, CpG islands, EST similarities, and repetitive elements withing DNA sequence

GRASTA
Purpose: format parser

HMMER
Purpose: Software suite for making and using Hidden Markov Models (HMMs) of biological sequences

ICATOOLS
Purpose: sequence project information generator

InterPRO-Scan
Purpose: protein function detector

LUCY
Purpose: Sequence Cleanup Program

Micropeats
Purpose: Sequence similarity search and visualization

MSPcrunch
Purpose: BLAST enhancement filter

MUMMER
Purpose: Program for fast alignment of large-scale DNA and protein sequences

PHRAP
Purpose:Sequence assembler

PHRED
Purpose: base-caller processor

REPEAT_MASKER
Purpose:Program which screens DNA sequences for interspersed repeats and low complexity DNA sequence

RePuter
Purpose:Fast Computation of Degenerative Repeats in Complete Genomes program

SPIDEY
Purpose: mRNA-to-genomic alignment program

STADEN
Purpose: sequence analyzer

STROLL
Purpose: Fragment assembly for large-scale genome sequencing

T-COFFEE
Purpose: Multiple sequence alignment program

TGICL
Purpose: Fast clustering of large EST datasets

TIGR_ASSEMBLER
Purpose: genome assembly tool

TIGR_COMBINER
Purpose: Combines the results of different gene prediction programs

TimeSearcher
Purpose: visual exploration of time-series data

Treemap
Purpose: space-constrained visulization of hierarchical structures

TRNA_SCAN
Purpose: tRNA identifier

XPP
Purpose: Tool for solving differential equations, difference equations, delay
equations, functional equations, boundary value problems and stochastic equations.

Purpose: automatic sequence annotatoin

Purpose: automatic download/update of GCG database

Purpose: automatic backup of the new sequences

gcc, g++
Purpose: GNU C, C++ compilers

g77
Purpose: GNU Fortran 77 compilers

java
Purpose: Java

perl
Purpose: Perl

python
Purpose: Python

BIOINFORMATICS SOFTWARE ON medusa.vcu.edu

BLAST
Purpose: Sequence similarity search program

NCBI-BLAST
WU-BLAST
NR
SWISSPROT

EMBOSS
Purpose: The European Molecular Biology Open Software Suite

FASTA
Purpose: Sequence similarity search program

GLIMMER
Purpose:Program for finding genes in microbial DNA, especially the genomes of bacteria and archaea

GLIMMERM
Purpose:A gene finder derived from Glimmer, but developed specifically for eukaryotes

OTHER PROGRAMS

gcc, g++
Purpose: GNU C, C++ compilers

perl
Purpose: Perl

BIOINFORMATICS SOFTWARE ON saga.vcu.edu

Arachne
Purpose: Whole Genome Assembly

ECELL
Purpose:Software environment for whole-cell simulation

GeneX
Purpose:Gene expression database and analysis software

RnaViz
Purpose:GUI program for producing publication-quality secondary structure drawings of RNA molecules

gcc, g++
Purpose: GNU C, C++ compilers

perl
Purpose: Perl

python
Purpose: Python

ActivePerl - Perl Programming environment

Adobe Acrobat Reader - This program displays Acrobat documents (extension .pdf).

Array Tools (DL key: BaXUZeGazEro) - Integrated software package for the analysis of DNA microarray data. It contains utilities for processing expression data from multiple arrays, visalization of data, multidimensional scaling, clustering of genes and samples, and classification of samples.

BioEdit - BioEdit is a biological sequence editor that runs in Windows 95/98/NT/2000 and is intended to provide basic functions for protein and nucleic sequence editing, alignment, manipulatoin and analysis.

BLAST Search - BLAST (Basic Local Alignment Search Tool) searches explore, using a DNA or protein query sequence, publicly available databases for sequence similarity. BLAST programs have been designed for speed, with a minimal sacrifice of sensitivity to distant sequence relationships. BLAST scores have a well-defined statistical interpretation, making real matches easy to distinguish from random background hits. BLAST uses a heuristic algorithm that seeks local as opposed to global alignments and is therefore able to detect relationships among sequences that share only isolated regions of similarity. (Altschul, et al. 1990).

Cellular Automata - A program that visualizes the interactions within a system (spread of disease, cells, etc.) given some set of rules.

CellAut> JCasIm - Simulates a disease outbreak, and allows the user to control the outcome.

Chime (http://www.mdli.com/chime/) - Simulates a disease outbreak, and allows the user to control the outcome.

Clustal X (ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/ )- A general purpose multiple alignment program for DNA or proteins, using a window interface for sequence input and display. * Windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results.

Cluster- Perform a variety of types of cluster analysis and other types of processing on large microarray datasets. Currently includes hierarchical clustering and self-organizing maps (SOMs).

Cn3D (NCBI)- Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service.

ContigExpress - ContigExpress is a program for assembling many small fragments, both text sequences and chromatograms from automated sequencers, into longer contiguous sequences or "contigs".

Cytoscape - A bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.

FluxAnalyzer - MATLAB ® (Mathworks, Inc.) package that aims at providing an comprehensive and user-friendly environment facilitating stoichiometric analyses of arbitrary chemical, in particular metabolic networks. The core concept of visualization and interactivity is realized by interactive flux maps where the abstract network model can be linked with network graphics.

Gene Codes> Sequencher (on CD)- The complete software solution for sequencing DNA.

GeneDoc - A Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows.

GhostScript - Allows the user to view PostScript files, as well as printing them on non-PostScript printers.

GSview/Ghost Gum - A graphical interface for Ghostscript.

Hierarchical Clustering Explorer - interactive exploration of multidimensional data

HostExplorer - Host Explorer provides host connectivity to the mainframe through TN3270 applications.

Maple 8 - Maple 8 is a comprehensive computer system for advanced mathematics. It includes facilities for interactive algebra, calculus, discrete mathematics, graphics, numerical computation and many other areas of mathematics. It also provides a unique environment for rapid development of mathematical programs using its vast library of built-in functions and operations.

MathLab 6.5 - MATLAB is a high-performance language for technical computing. It integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation.

MATreeView - Program for displaying phylogenies

Microsoft Internet Explorer - An internet web brower.

Microsoft Office XP - Microsoft Office desktop suite containing Word, Excel, Outlook, PowerPoint, and Access.

Netscape- An internet web browser.

Phylip - Package of prgrams for inferring phylogenies

Real Player - A media player that runs Real Media files (extensions .rm and .ram).

SSH Secure Shell Client - The SSH Secure Shell for Workstations Windows client is a program that allows secure network services, such as telnet or ftp, over an insecure network.

TreeView - TreeView provides a simple way to view the contents of a NEXUS, PHYLIP, Hennig86, Clustal, or other format tree file.

UTHSCSA ImageTool (IT) - Image processing and analysis program for Microsoft Windows that can acquire, display, edit, analyze, process, compress, save and print gray scale and color images. Reads and writes over 22 common file formats. Includes dimensional (distance, angle, perimeter, area) and gray scale measurements (point, line and area histogram with statistics), standard image processing functions (contrast manipulation, sharpening, smoothing, edge detection, median filtering) and spatial convolutions with user-defined convolution masks. IT also has built-in scripting capabilities that allow the user to record repetitive tasks and playback saved scripts to automate image analysis.

Vector NTI Suite 6

3D-Mol - The Vector NTI Suite application used for visualization and analysis of three-dimensional information derived from PDB structures or structures created by user. The 3D viewer is designed to simplify viewing and analyzing of tertiary structures of proteins, nucleic acids and small organic and inorganic molecules. The viewer currently allows the display molecules saved in PDB and M3D formats.

AlignX - The multiple sequence alignment application, AlignX, of the Vector NTI Suite is a comprehensive program designed to conduct and manage multiple sequence alignment projects. Based on the Clustal W algorithm, Align X incorporates all of the following features:

Phylogenetic tree construction, displayed in graphical representation

Use of residue substitution matrices

Secondary structure consideration

Multicolored alignment presentation

Automatic consensus calculationFull alignment editing capabilities

Dot matrix comparison of any two sequences

AlignX Blocks - AlignX Blocks is a program for locating, analyzing, and editing blocks of localized sequence similarity among multiple protein sequences and linking them into a composite multiple alignment.

Back Translation - The Back Translate feature from the Vector NTI Suite allows you to obtain a DNA sequence from a protein sequence by reversing the translation process. The codon usage can be set by selecting any of the options from the drop down menu in the Back Translation dialog box. The ambiguity is defined by a codon usage table. There are a number of pre-set codon usage settings available.

BioPlot - BioPlot is a sequence analyzer that performs certain types of DNA and protein sequence analyses, and displays the results as linear graphics. For proteins, amino acid scaling allows the user to visualize the distribution of the particular physio-chemical properties along the polypeptide chain, thus providing helpful hints about the functional properties of the protein regions or domains. An amino acid scale is defined by a numerical value assigned to each type of amino acid. The most frequently used scales are the hydrophobicity, hydrophilicity, and the secondary structure conformational parameters scales, but many other scales exist which are based on different chemical and physical properties of the amino acids. This program provides approximately 60 predefined scales entered from the literature.

BLAST Viewer - BLAST (Basic Local Alignment Search Tool) searches explore, using a DNA or protein query sequence, all of the available sequence databases at the NCBI (National Center for Biotechnology Inormation) for sequence similarity. For details regarding the Vector NTI Suite BLAST Search feature, refer to that application’s Online Help or the User’s Manual.

Citation Viewer - This feature of the Vector NTI Suite provides a vehicle for displaying and reviewing citation abstracts downloaded by PubMed Search or created manually and stored in the Vector NTI database or local file. Citations can be printed, edited and saved from Citation Viewer.

Database Explorer - This program supports BLAST results and Literature Citations. Support for literature citations make the VNTI suite a complete Bibliographic package, much like EndNote etc., but with integrated search facilities (PubMed-Entrez Search). It can be used to insert references in documents when writing a journal article or other document and it can format those citations in more than a 100 journal specific styles. Citation are copied in the document as temporary tags and after the document has been finished, the document is converted and the temporary tags are replaced with the journal-specific style and a list of references is appended to the end of the document.

GCG File Converter - A utility to convert GCG formatted files into a format that VNTI can read.

Matrix Editor - This utility will allow the user to create and edit scoring matrices used by AlignX and AlignX Blocks. In addition, it features the calculator for the Lambda and Kappa parameters used in calculating the statistical significance of high-scoring segments or sub-alignments.

PubMed/Entrez Search - This feature of the Vector NTI Suite is a client program for the NCBI Entrez/PubMed search engines. Database searches are performed in much the same way they are in the NCBI website: through the PubMed/Entrez Search Tool, you send a user query to Entrez/PubMed. The convenience of this Vector NTI Suite tool lies in its connectivity to the internet and its ability to retrieve and list the results. From this list, you can easily view the results in either a Molecule Display window or the Citation Viewerand store them in the Vector NTI Suite database.

Tools Manager - The menu bar of all VNTI programs can be extended with custom menus. The Tools manager can be used to set up the menus. The menu items can be any program or script and parameters and data from VNTI can be passed to the programs. The menu items can be made active depending on the type of data currently selected, so only the menu items that pertain to the item that is selected in a VNTI program will be active.

Vector NTI Database - An analysis and data management software application for molecular biology research. It provides an onboard database for the storage and organization of clones, vectors, fragments, primers, proteins, peptides, gel markers, and restriction enzymes, as well as the analys tools to study a molecular structure, function, nucleotide sequence, open reading frames, and more.

WS FTP - A file transfer client.

XPP
Purpose: Tool for solving differential equations, difference equations, delay
equations, functional equations, boundary value problems and stochastic equations.

X-Win 32 - Win32 is a PC X server for connecting Windows PCs with UNIX servers including Sun Solaris, HP/UX, IBM AIX, SCO, FreeBSD, as well as Linux machines.

nr - non redundant protein database (AA format)

Pfam - protein families database

UniVec - vector sequences database

ecoli- ecoli sequence database

go - gene ontology database

halfwise - created from the Pfam FULL alignments, used by GeneWise

mito- mitochondrial protein database

RefSeq- NCBI's non redundant DNA, RNA, and protein sequences database

nr,nt - non redundant protein database (AA, DNA format)

swall - swissprot + trembl protein database

BCCL Teaching Lab

Dell Dimension XPS-2 532, 568 Ram

BIND
Purpose: BIND is an expanding database of biomolecular interaction, pathway and complex information. All information is stored in BIND database records that are freely available through a web interface that allows users to query, view, and submit records.

DATA ALIVE
Purpose:Integrated database system for the computational analysis and visualization of biochemical pathways.

DIP
Purpose: Database of experimentally determined interactions between proteins

GRAVISTO
Purpose: Gravisto is an editor for graphs and a toolkit for implementing graph visualization algorithms

PathBlast
Searches the yeast protein-protein interaction network to identify all protein interaction pathways that align with a pathway query.

PROTEOME-3D
An interactive bioinformatics tool for large-scale data exploration and knowledge discovery. Features: 1) creation of a scalable, queryable, customized database for identified proteins from published literature 2) graphicaltools for displaying proteome landscapes and trends from multiplelarge-scale experiments 3) interactive data analysis that facilitates identification of crucial networks and pathway

TRIPLES
Purpose: Online database of TRansposon-Insertion Phenotypes, Localization, and Expression in Saccharomyces

UMass Chime
Purpose: Molecular Visualization Resources

WebVAR
Purpose: Web server to provide site specific estimates of relative site variability from fasta format multiple sequence alignments.

YMGV
Purpose:Online database for visualization and data mining of published genome-wide yeast expression data