In the public domain

Abstract

Wonderful as web tools for molecular biology may be, eventually the working scientist must interrupt his or her play with Java Applets, Active-X Buttons, and other such gizmos, and get down to some serious computational molecular biology on his or her own computer. Even here, the web can come in handy, as there are many archives of biological software out there. These act as repositories for ‘public domain’ or ‘shareware’ programs, and also carry reviews or comparisons of commercial offerings. Rather than trying to cover this enormous field in detail, here is a collection of pointers to some of the best resources. Several companies claim to offer ‘comprehensive solutions’ for the molecular biologist's sequence manipulation needs — at a price. Typically, these packages offer restriction-site mapping, contig assembly for sequencing, backwards and forwards translation of DNA sequences, multiple sequence alignment, and much (often, too much) more. Some companies have product information on the web — for example, Geneworks (http://www.ig.com/PRODUCTS/genew_top.html) and PC/GENE (http://www.ig.com/PRODUCTS/pcgene_top.html). There is a good list at http://www.hslib.washington.edu/hsl/bioinfo/software.html. Primer design programs can predict the appropriate temperature for primer annealing and can warn of potential problems with dimerization and hairpin loop formation. Most commercial integrated packages offer primer design, but there are also plenty of free options. There is a good list of primer design programs at the PCR Jump Station (http://www.apollo.co.uk/a/pcr/#pcrs). For die-hard web-users, one of the standard programs, called simply ‘primer’, has been converted into a Java applet by Luca Toldo, so it can be used over the web. It can be found at http://www.embl-heidelberg.de/∼toldo/JaMBW/5/2/index.html. It runs about six-times slower than the normal version, but will work on whatever machine you use — Mac, PC or UNIX — as long as it supports Java. The Department of Genetics of Washington University has a fantastically comprehensive list of programs for the analysis and visualization of phylogenetic relationships (http://evolution.genetics.washington.edu/software.html). It lists more than 80 programs, categorizes them by algorithm and by the computer system on which they run, and provides an excellent evaluation of the strengths and weaknesses of each. Highly recommended. The Protein Databank maintains a list of software (mostly free) for analysing, visualizing, and manipulating proteins structures (http://pdb.pdb.bnl.gov/software.html). A good list of biological software archives is held at Johns Hopkins University (http://www.gdb.org/Dan/softsearch/biol-links.html). Two of the biggest archives it lists are at Indiana University (ftp://ftp.bio.indiana.edu/) and the European Bioinformatics Institute (EBI; http://www.ebi.ac.uk/software/software.html). The software descriptions in the archive at the EBI are fully searchable (http://www.gdb.org/Dan/softsearch/softsearch.html). Bibliographic software is indispensable for the modern biologist. With new packages coming on to the market all the time, the choice can be bewildering, so take a look at the beginner's guide at http://www.chorus.cycor.ca/biblio/biblio1.html. This site also offers up-to-date comparative evaluation of available programs. [email protected] URLs (http://… etc.) can be typed directly into a web browser such as Netscape. A list of the ‘web words’ used in this article can be found in Current Biology 6:494 or its electronic equivalent athttp://BioMedNet.com/ Geneworks PC/GENE List of commercial packages PCR Jump Station ‘Primer’ Java applet Washington University phylogenetics list Protein Databank structural biology list Johns Hopkins University archive list Indiana University software archive European Bioinformatics Institute software archive Searchable software at EBI Beginner's guide to bibliographic software