BLAST ( Basic Local Alignment Search Tool) comes under the category of homology and similarity tools. It is a set of search programs designed for the Windows platform and is used to
perform fast similarity searches regardless of whether the query is for protein or DNA. Comparison of nucleotide sequences in a database can be performed. Also a protein database can be searched to find a match against the queried protein sequence. NCBI has also introduced the new queuing system to BLAST (Q BLAST) that allows users to retrieve results at their convenience and format their results multiple times with different formatting options.
EMBOSS (European Molecular Biology Open Software Suite) is a software-analysis package. It can work with data in a range of formats and also retrieve sequence data transparently from the Web. Extensive libraries are also provided with this package, allowing other scientists to release their software as open source. It provides a set of sequence-analysis programs, and also supports all UNIX platforms.
It is a fully automated sequence alignment tool for DNA and protein sequences. It returns the best match over a total length of input sequences, be it a protein or a nucleic acid.
It is a powerful research tool to display the structure of DNA, proteins, and smaller molecules. Protein Explorer, a derivative of RasMol, is an easier to use program.
PROSPECT (PROtein Structure Prediction and Evaluation Computer ToolKit) is a protein-structure prediction system that employs a computational technique called protein threading to construct a protein's 3-D model.
PatternHunter, based on Java, can identify all approximate repeats in a complete genome in a short time using little memory on a desktop computer. Its features are its advanced patented algorithm and data structures, and the java language used to create it. The Java language version of PatternHunter is just 40 KB, only 1% the size of Blast, while offering a large portion of its functionality.
