There are a number of really useful bioinformatics tools freely available on the Internet. While many commercial products exist that may be more complete or provide extra tools, they are often expensive and do not justify the cost with their added benefits. Below is a list of some of the best and most complete free bioinformatics resources.
1) NCBI Tools for Bioinformatics Research (http://www.ncbi.nlm.nih.gov/Tools/)
The National Center for Biotechnology Information maintains an array of very powerful tools for sequence analysis, gene model building, finding open reading frames, and aligning RNA, DNA or protein sequences. There are over two dozen pieces of software available, some for download and others run right in your browser. The most famous of the NCBI tools is the BLAST suite, which allows for sequence alignments and comparison. The various flavors of BLAST let the user compare protein, RNA and DNA sequences.
2) European Bioinformatics Institute (http://www.ebi.ac.uk/Tools/)
Analogous to the NCBI bioinformatics suite, the EBI’s resources provide an array of tools and databases for scientists. The EBI began with the forming of the EMBL Nucleotide Sequence Library, which was the world’s first sequence database. Soon after, the EBI was formed and tools were developed to be used in conjunction with the sequence database. One of the most well-known tools at the EBI is ClustalW, which is used to build genetic and evolutionary phylogenies from gene sequences.
3) Protein Databank (http://www.pdb.org/pdb/home/home.do)
The PDB provides many structures of proteins, DNA and RNA. These structures are freely available for use by other researchers. The databank recently surpassed 50,000 structures.
4) SCFBIO (http://www.scfbio-iitd.res.in/bioinformatics/bioinformaticssoftware.htm)
The SuperComputing Facility for Bioinformatics and Computational Biology provides a set of tools vastly different from those at the EBI or NCBI. Included with some basic sequence analysis programs is a set of tools for structure prediction, protein-protein docking, structure optimization and gene finding. There is overlap with the other bioinformatics tools, but the structure and docking prediction algorithms provide new insight into any analysis of a protein.
5) PredictProtein (http://www.predictprotein.org/main.php)
This program predicts the secondary structure of a given protein sequence with some accuracy.
6) ORNL (http://compbio.ornl.gov/)
Computational Biology at the Oak Ridge National Laboratory has a set of useful tools including GrailExp, which predicts genes, introns, exons, promoters, CpG islands and repetitive elements in a sequence.
7) Genes@MIT (http://genes.mit.edu/)
The Genes server at MIT provides a number of useful tools, including GENSCAN and FAS-ESS, which predicts exonic splicing silencers.