Similarity searching tools

Sequence similarity search tools Alignments of the query sequence with databases produce sequence similarity. The BLAST series of programs has variants that will translate DNA databases, translate the input sequence, or both. FASTA provides a similar suite of programs. 

Searching for compounds in databases that are similar to query molecules is one of the most widely applied molecular similarity-based approaches. Commonly used similarity search tools have different levels of complexity, as discussed in the following. 

PubChem is organized as three linked databases within the NC8I s Entrez information retrieval system. These are PubChem Substance. PubChem Compound, and PubChem BioAssay. Pubchem also provides a fast chemical structure similarity search tool. More information about using each component database may be found using the links above. 

BLAST Basic Local Alignment Search Tool is the most popular nucleotide and protein similarity searching tool in bioinformatics. It is web-accessible, free, fast, and can search many databases at the same time. It can detect isolated sequence patterns, especially if used with the more recent position-specific iterative method PSI-BLAST. Similarity of residues can be defined via mutation or physicochemical substitution matrices. 

National Center for Biotechnology Information (Bethesda, MD) BLAST sequence similarity search tools http //www.ncbi..nml.nih.gov /BLAST/... 

In the LEVS field, one can broadly distinguish between two basic categories of methods similarity searching on one hand and compound classification on the other [3]. The popular similarity search tools as shown in Figure 11.1 include molecular fingerprints derived from molecular graphs (2D) or conformations (3D) [4, 5], pharmacophore models [6], simplified molecular graph representations [7],... 

Although similarity search tools can be applied on the basis of individual reference molecules, their performance generally increases when multiple reference compounds are available, which then makes it possible to apply data fusion techniques to merge individual results [19]. Generally, the chemical information content of search calculations is increasing with the availability of multiple active reference compounds. 

Similarity search appears as an extremely useful tool for computer-aided structure elucidation as well as for molecular design. Here the similarity property principle is involved. This may be stated as ... 

Similarity search appears as an extremely useful tool for computer-aided structure elucidation as well as molecular design. 

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. 

Grethe G, Moock TE. Similarity searching in REACCS. A new tool for the synthetic chemist. / Chem Inf Comput Sci 1990 30 511-20. 

ExPASy Proteomics tools (http //expasy.org/tools/), tools and online programs for protein identification and characterization, similarity searches, pattern and profile searches, posttranslational modification prediction, topology prediction, primary structure analysis, or secondary and tertiary structure prediction. 

The second postprocessing step is the automated enhancement of the TrEMBL annotation to bring TrEMBL entries closer to SWISS-PROT standard. There is an increasing need for reliable automatic functional annotation to cope with the rapidly increasing amount of sequence data. Most of the current approaches are still based on sequence similarity searches against known proteins. Some groups try to collect the results of different prediction tools in a simple way, e.g., PEDANT (Frishman and Mewes, 1997) or GeneQuiz (Scharf et al., 1994). However, several pitfalls of these methods have been reported (Bork and Koonin, 1998). 

This section focuses on the use of SWISS-PROT + TrEMBL for sequence similarity searches. Searches in protein sequence databases have now become a standard research tool in the life sciences. To produce valuable results, the source databases should be comprehensive, nonredundant, well annotated, and up-to-date. However, lack of a single protein sequence database that satisfies all four criteria has previously forced users to perform searches across multiple databases to avoid incomplete results. This strategy normally produces complete but redundant results owing to different versions of the same sequence report in different databases. 

Sequence similarity searching Basic Local Alignment Search Tool (BLAST) http //www.ncbi.nlm.nih.gov/BLAST/ Comparison of novel sequences with known genes. 

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