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Download Protein Sequence Databases
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MOLECULAR DATABASE Biological databases are stores of biological information. The journal Nucleic Acids Research regularly publishes special issues on biological databases and has a list of such databases. Protein Sequence Databases In the field of bioinformatics, a sequence database is a type of biological database that is composed of a large collection of computerized ("digital") nucleic acid sequences, protein sequences, or other polymer sequences stored on a computer. The UniProt database is an example of a protein sequence database. Sequence databases can be searched using a variety of methods. The most common usage is probably searching for sequences similar to a certain target protein or gene whose sequence is already known to the user. The BLAST program is a popular method of this type. BLAST In bioinformatics, BLAST for Basic Local Alignment Search Tool is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. Using a heuristic method, BLAST finds similar sequences, by locating short matches between the two sequences. This process of finding similar sequences is called seeding. FASTA FASTA is a DNA and protein sequence alignment software package first described (as FASTP) by David J. Lipman and William R. Pearson in 1985. FASTA is pronounced "fast A", and stands for "FAST-All", because it works with any alphabet. FASTA takes a given nucleotide or amino acid sequence and searches a corresponding sequence database by using local sequence alignment to find matches of similar database sequences. The FASTA program follows a largely heuristic method which contributes to the high speed of its execution. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. Protein Structure Databases In biology, a protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way. Data included in protein structure databases often includes three-dimensional coordinates as well as experimental information, such as unit cell dimensions and angles for x-ray crystallography determined structures. Though most instances, in this case either proteins or a specific structure determinations of a protein, also contain sequence information and some databases even provide means for performing sequence based queries, the primary attribute of a structure database is structural information, whereas sequence databases focus on sequence information, and contain no structural information for the majority of entries. SEQUENCE ALIGNMENT In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. 1. Pairwise alignment: Pairwise sequence alignment methods are used to find the best-matching piecewise (local) or global alignments of two query sequences. Pairwise alignments can only be used between two sequences at a time, but they are efficient to calculate and are often used for methods that do not require extreme. The three primary methods of producing pairwise alignments are i. dot-matrix methods, ii. dynamic programming, and iii. word methods 2. Multiple sequence alignment: Multiple sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time. Multiple alignment methods try to align all of the sequences in a given query set. Multiple alignments are often used in identifying conserved sequence regions across a group of sequences hypothesized to be evolutionarily related. Such conserved sequence motifs can be used in conjunction with structural and mechanistic information to locate the catalytic active sites of enzymes. The methods of producing Multiple sequence alignment are: i. Dynamic programming ii. Progressive methods iii. Iterative methods iv. Motif finding v. Techniques inspired by computer science