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| Science & Tech /Software /Molecular Biology / |
The CMS-SDSC Molecular Biology Resource
Excellent compendium of Internet-accessible analytical tools & resources for Molecular Biology, Biotechnology, Molecular Evolution, Biochemistry, and Biomolecular Modeling from the UCSD Supercomputer Center.
(http://www.unl.edu/stc-95/ResTools/cmshpb.html)
Transcription Element Search Software (TESS)
Very helpful software for locating and displaying transcription factor binding sites within DNA sequences - from the Univ. of Penn.
(http://www.cbil.upenn.edu/tess/index.html)
Amphi Program
This program provides algorithms to calculate three amphipathic characteristics of a given amino acid sequence: (i) the hydrophobicity of segments of 7 amino acid residues,(ii) the hydrophobicity of segments of 19 amino acid residues, (iii) the amphipathy
(ftp://ftp.bchs.uh.edu/pub/gene-server/vms/amphi.uue)
bionet.software.acedb newsgroup archive
discussions by users of genome DBs using ACEDB
(http://www.bio.net/hypermail/ACEDB/)
bionet.software.gcg newsgroup archive
discussions about using the GCG software
(http://www.bio.net/hypermail/INFO-GCG/)
Bioperl
public domain Perl tools for computational molecular biology
(bio.perl.org/)
BioScience Research Tool: Databases
Excellent specialized directory of online tools and resources selected mainly for Molecular Geneticists.
(biochemie.net/links/Databases/)
CloneMap version 2.11
a complete solution for fast and easy plasmid map drawing,restriction site mapping, and virtual cloning.
(http://www.cgcsci.com/cminfo.shtml)
Combinatorial Extension of Polypeptides
Method for finding 3-D similarities in protein structures from the UCSD Supercomputer Center.
(cl.sdsc.edu/ce.html)
Entrez Browser
retrieves molecular biology data and bibliographic citations from the NCBI's integrated databases.
(http://www.ncbi.nlm.nih.gov/Entrez/)
Equilibrate Web site
Equilibrate software can be used as a scientific or educational tool in biochemistry and molecular biology for quantitative analysis of molecular interactions. This includes calculation of the steady state equilibrium, calculation of the dissociation con
(http://www.erols.com/gjcv/index.html)
Forager
PC software that calculates equilibria of molecules that physically interact with each other.
(http://www.amberwaves.com/forager/forager.htm)
Free Software for Molecular Biology
Gopher site listing over 150 free software programs in molecular biology and related areas - from Indiana Univ. Program files found at: gopher://iubio.bio.indiana.edu:70/11/IUBio-Software+Data/molbio.
(gopher://iubio.bio.indiana.edu:70/h0/IUBio-Software+Data/molbio/Listings.html)
Functional Genomics
Online programs for predicting biological function of genes and proteins from their primary sequence, predicting structure of protein and DNA from its sequence motifs, and understanding how and when genes are expressed - from Stanford Univ.
(http://motif.stanford.edu)
GeneDoc
a full featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows.
(http://www.cris.com/~ketchup/genedoc.shtml)
Genomica Corporation
BioPharmaceutical software for functional genomics, gene discovery, and positional cloning; using genetic analysis, physical mapping, and sequence analysis.
(http://www.genomica.com)
MacPlasmap version 2.1
an easy-to-use color drawing program for preparation of circular and linear plasmid maps.
(http://www.cgcsci.com/mpminfo.shtml)
Melanie II 2-D Analysis Software
Powerful, state-of-the-art, 2-D analysis software package with user-friendly interface from the Swiss Institute of Bioinformatics (SIB).
(http://www.expasy.ch/melanie/)
Molecular Biology Computation Resources (MBCR)
Includes the MBCR Guide to Computer Aided Sequence Analysis, homology searching, databases, & lists of useful links for molecular biologists - from the Baylor College of Medicine.
(http://mbcr.bcm.tmc.edu/)
Oligo Software
Oligo software is a Molecular Biology Insights product. It has been created for difficult sequencing and PCR primer design projects. First on the market (1989).
(http://www.oligo.net/)
OxMol MacVector
a comprehensive set of fully integrated sequence analysis functions for Apple Macintosh
(http://www.oxmol.co.uk/prods/macvector/)
Plasmid Processor
a simple tool for plasmid presentation for scientific and educational purposes.
(http://www.hytti.uku.fi/~kiviraum/plasmid/plasmid.html)
Proteomics Tools
Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB).
(http://www.expasy.ch/tools/)
SigmaScan Pro-Powerful Image Analysis for Your PC
SigmaScan Pro 5.0 provides a complete image analysis package for studying the structure and size of objects in your visual information.
(http://www.spss.com/software/science/sigmascan)
Swiss-Model
Automated comparative protein modelling server to make protein modelling accessible to biochemists and molecular biologists worldwide - from GlaxoWellcome Experimental Research, Geneva, Switzerland.
(http://www.expasy.ch/swissmod/SWISS-MODEL.html)
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