Sequence similarity search 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. 

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

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. 

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. 

Figure 11,4. ExPASy Proteomic tools. ExPASy server provides various tools for proteomic analysis which can be accessed from ExPASy Proteomic tools. These tools (locals or hyperlinks) include Protein identification and characterization, Translation from DNA sequences to protein sequences. Similarity searches, Pattern and profile searches, Post-translational modification prediction, Primary structure analysis, Secondary structure prediction, Tertiary structure inference, Transmembrane region detection, and Sequence alignment.

Whitney, J Esteban, D. J., and Upton, C. (2005) Recent Hits Acquired by BLAST (ReHAB) a tool to identity new hits in sequence similarity searches. BMC Bioinformatics 6, 23. 

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. 

Worley KC, Wiese BA, Smith RF. BEAUTY An enhanced BLASTbased search tool that integrates multiple biological information resources into sequence similarity search results. 

W. R. Pearson and D. J. Lipman, Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85, 2444—2448 W. R. Pearson, Empirical statistical estimates for sequence similarity searches. J. Mol. Biol. 276, 71-84 (1998). 

Another useful structure tool is RasMol (or RasMac). This will allow you to view the detailed structure of a protein and rotate it on coordinates so you can see it from all perspectives. A hyperlink to RasMol is present under the View Structure function just above Chime. You may need to study RasMol instructions provided under Help, or you may use a Ra.s Mol tutorial listed in Table El.2. Another useful protein viewer is tin-Swiss-Protein Pdv Viewer (Table El.2). BLAST is an advanced sequence similarity tool available at NCBI. To access this, go to the NCBI home page (www.ncbi.nlm.nih.gov) and click on BLAST. Then click on Basic BLAST search to obtain a dialogue box into which you may type the amino acid sequence of human a-lactalbumin. This process may be stream lined by downloading the amino acid sequence in FASTA format into a file and transferring the fde into the BLAST dialogue box. BLAST will provide a list of proteins with sequences similar to the one entered. 

A sequence alignment is a way of determining the similarity between two strings. This is a classical question in computer science, and has an exact solution referred to as the Smith/Waterman alignment. Unfortunately, this exact solution can be slow when analyzing large sequences, and therefore, approximate methods, such as Basic Local Alignment Search Tool (BLAST), have been developed to identify very similar sequences. 

BLAST Basic Local Alignment Search Tool. One of the more widely used tools in genome informatics, for similarity searches of protein or DNA sequences. 

Software tools for database searching and available protein sequence databases for protein identification were reviewed [130-131], Liska and Shevchenko [132] reviewed approaches to study proteomes with nonsequenced genomes via sequence similarity database searching. 

Therefore, and also to compare the results with existing information, one may still want to search the database with the results obtained by de novo sequencing. The approach to follow is a BLAST search (Basic Local Alignment Search Tool, [133-134]). Sequence alignment is a powerful way to compare novel sequences with previously characterized sequences and search for similarities. The BLAST search is much slower than the database searches outlined in Ch. 17.6.2. A nice example is the de novo identification of the bacterium Shewanella putrefaciens proteome by 2D-GE, in-gel digestion, direct infusion nano-ESl, and nano-LC-MS [135]. The results were BLAST searched against the incomplete genome of the bacterium. 

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