BLAST search algorithm

All of the three IC centers also provide facilities for sequence similarity search and alignment. The widely used database search algorithms are FASTA (Lipman and Pearson, 1985) at http //www.nbrf.georgetown.edu/pirwww/search/fasta.html and BLAST (Altschul et al., 1990) at http //www.ncbi.nlm.nih.gov/BLAST/. For BLAST... 

For these reasons, it is important to focus on the most divergent set of superfamily members that can be identified. Although a variety of new methods have recently been developed for identification of distantly related protein sequences [see, for example, Psi-Blast (Altschul et al, 1997), methods based on Hidden Markov Models such as SAMT98 (Kar-plus et al., 1998), the Intermediate Sequence Search algorithm of Park et al., (Park et al., 1997), or the simple congruence method, Shotgun (Pegg and Babbitt, 1999)], confirmation of these relationships can be technically difficult. In some cases, three-dimensional structural information or experimental structure-function analysis will be required to pro-... 

The fact that a profile or HMM can pick out new sequences also related to the given family suggests that these should be used to update the profile or HMM used as search pattern. This idea leads to iterative search algorithms where the database is searched repeatedly, each time updating the query pattern with some or all of the newly identified sequences. Psi-Blast [101] is a very successful implementation of this idea. It starts with a single... 

The aim of the fust dimension breadth is to reveal sequence-function relationships by comparing protein sequences by sequence similarity. Simple bioinformatic algorithms can be used to compare a pair of related proteins or for sequence similarity searches e.g., BLAST (Basic Local Alignment Search Tool). Improved algorithms allow multiple alignments of larger number of proteins and extraction of consensus sequence pattern and sequence profiles or structural templates, which can be related to some functions, see e.g., under http //www. expasy.ch/tools/ similarity. 

Bioinformadcs has invaded most wet-lab environments, where databank searches in Genbank and PubMed, and thus algorithms such as blast, have become indispensable tools in the daily routine. This is largely due to the fact that the most often used services are available as convenient web applications and require little or no thought about such details as getting and ins tailing software or reading technical manuals. 

PSI-)BLAST Algorithm for searching of nucleotide and protein databases 26 www.ncbi.nlm.nih.gov/BLAST/... 

---