BLAST searches Search Tool

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. 

BLAST basic local alignment search tool... 

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

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. 

Finally, the goal of this first phase is to analyze and to compare the resulting proteins and peptides by alignment search tools, such as BLAST (http / blast.ncbi.nlm.nih.gov/Blast.cgi CMD=Web PAGE TYPE=BlastHome), in order to identify and characterize specific peptide fingerprints, which will be used in the monitoring approach of the next phase of the pipeline. 

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. 

Putative functional domains within the uncharacterized protein can be identified using the CDD search tools while performing protein-protein BLAST (BLASTP) alignments to obtain insight into possible functions of the predicted protein. The predicted protein sequence is used since amino-acid sequences are more evolutionarily conserved than nucleotide sequences, and therefore a broader search across all available sequence information from a variety of organisms can be conducted to identify potential functionality. Results from the BLASTP and CDD analysis (Fig. 10) have identified... 

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. 

This chapter is informally divided into two parts. The first part is devoted to sequence comparisons and culminates in the database search tool BLAST. The second part considers the analysis of population-level data, providing sufficient background to understand how genes influencing traits such as response to toxicity may be located within the genome. 

Lost in the above discussion is an unfortunate truth Even with DP, it takes too long to rigorously align a query sequence to each of the member sequences of a database. Because of this, database search tools seek approximations to the optimal local alignment, negotiating a balance between quality and speed with each comparison. This tradeoff and its implications are central to forthcoming discussion of the database search tool BLAST hosted at NCBI. 

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

The National Center for Biotechnology Information (NCBI). Located at the National Library of Medicine in Bethesda, MD, USA. The home of the GenBank DNA sequence database PubMed literature search engine sequence search tools (e.g., PSI-BLAST) genomic sequence navigation tools. A substantial repository of resources in all areas of bioinformatics. 

The most popular tool currently in use is BLAST (Basic Local Alignment Search Tool) (3 7) from the NCBI. BLAST is an example of a heuristic that attempts to optimize a specific similarity measure. The most recent revisions to the algorithm are gapped BLAST and PSI-BLAST (38), with improved accuracy for PSI-BLAST using composition-based statistics... 

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