BLAST [Basic Alignment Local Search Tool]

BLASTBasic Local Alignment Search Tool

National Center for Biotechnology Information (NCBI)

Fundamental ways of learning about a protein or gene

The search reveals what related sequences are present in the same organism and other organisms.

BLASTTypically, this means that millions of alignments are

analyzed in a BLAST search, and only the most closely related matches are returned.

Query sequence

Target SequenceNeedleman–Wunsch (1970)

Because we are usually more interested in identifying locally matching regions such as protein domains.

Query sequence

Target SequenceSmith–Waterman (1981)

we cannot generally use it for database searches because it is too computationally intensive.

Query sequence

Target SequenceBLAST

offers a local alignment strategy having both speed and sensitivity. It also offers convenient accessibility on the WorldWideWeb.

Family

Programs

Query sequence Target Sequence

A DNA sequence can be converted into six potential proteins, and the BLAST algorithms include strategies to compare protein sequences to dynamically translated DNA databases or vice versa.

The programs produce high-scoring segment pairs (HSPs) that represent local alignments between your query and database sequences.

BLAST1. Determining what orthologs and paralogs are known for a

particular protein or nucleic acid sequence.2. Determining what proteins or genes are present in a

particular organism.3. Determining the identity of a DNA or protein sequence.4. Discovering new genes.5. Determining what variants have been described for a

particular gene or protein.6. Investigating expressed sequence tags that may exhibit

alternative splicing.7. Exploring amino acid residues that are important in the

function and/or structure of a protein

BLAST1. Selecting a sequence of interest and pasting, typing, or

uploading it into the BLAST input box.2. Selecting a BLAST program (most commonly blastp, blastn,

blastx, tblastx,blastn).3. Selecting a database to search. A common choice is the non

redundant (nr) database, but there are many other databases.

4. Selecting optional parameters, both for the search and for the format of the output. These options include choosing a substitution matrix, filtering of low complexity sequences, and restricting the search to a particular set of organisms.

BLAST SEARCH STEPS1. Step 1: Specifying Sequence of Interest:

First Cutting and pasting DNA or protein sequence (e.g., in the FASTA format).

Second using an accession number (e.g., a RefSeq or GenBank Identification [GI] number)

BLAST searches, your query can be in uppercase or lowercase, with or without intervening spaces or numbers.

If the query is DNA, BLAST algorithms will search both strands. It is often convenient to input the accession number to a BLAST

search.

BLAST SEARCH STEPS1. Step 2: Selecting BLAST Program

Program Query Number of database searches DatabaseBlastp protein proteinUse blastp to compare a protein query to a database of proteins

Blastn DNA DNAUse blastn to compare both strands of a DNA query against a DNA database.

Blastx DNA proteinBlastx translates a DNA sequence into six protein sequences using all six possible reading frames, and then compares each of these proteins to a protein database

tBlastn protein DNATblastn is used to translate every DNA sequence in a database into six potential proteins, and then to compare your protein query against each of those translated proteins.

tBlastx DNA DNATblastx is the most computational intensive BLAST algorithm. It translates DNA from both a query and a database into six potential proteins, and then performs 36 protein-protein database searches.

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BLAST [Basic Alignment Local Search Tool]

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