Introduction to BLAST, its Types & Homepage | Lecture 2, Part 1 by Dr. Muhammad Naveed

BLAST, Introduction, Types, NCBI, FASTA: In bioinformatics, BLAST (basic local alignment search tool) is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query) with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. Different types of BLASTs are available according to the query sequences and the target databases. For example, following the discovery of a previously unknown gene in the mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence. BLAST is actually a family of programs (all included in the blastall executable). These include: Nucleotide-nucleotide BLAST (blastn) This program, given a DNA query, returns the most similar DNA sequences from the DNA database that the user specifies. Protein-protein BLAST (blastp) This program, given a protein query, returns the most similar protein sequences from the protein database that the user specifies. Position-Specific Iterative BLAST (PSI-BLAST) (blastpgp) This program is used to find distant relatives of a protein. First, a list of all closely related proteins is created. These proteins are combined into a general "profile" sequence, which summarises significant features present in these sequences. A query against the protein database is then run using this profile, and a larger group of proteins is found. This larger group is used to construct another profile, and the process is repeated. By including related proteins in the search, PSI-BLAST is much more sensitive in picking up distant evolutionary relationships than a standard protein-protein BLAST. Nucleotide 6-frame translation-protein (blastx) This program compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database. Nucleotide 6-frame translation-nucleotide 6-frame translation (tblastx) This program is the slowest of the BLAST family. It translates the query nucleotide sequence in all six possible frames and compares it against the six-frame translations of a nucleotide sequence database. The purpose of tblastx is to find very distant relationships between nucleotide sequences. Protein-nucleotide 6-frame translation (tblastn) This program compares a protein query against the all six reading frames of a nucleotide sequence database. Large numbers of query sequences (megablast) When comparing large numbers of input sequences via the command-line BLAST, "megablast" is much faster than running BLAST multiple times. It concatenates many input sequences together to form a large sequence before searching the BLAST database, then post-analyzes the search results to glean individual alignments and statistical values. #NCBI_Blast #BLASTn #Input_sequence