Question

BLAST searches and related applications are essential for analyzing gene and protein sequences. Define BLAST, describe basic features of this bioinformatics tool, and provide an example of information provided by a BLAST search.

Short answer

In summary, BLAST is an essential algorithm in bioinformatics that aids in identifying homologous sequences, inferring function, detecting conserved domains, and studying evolutionary relationships among genes and proteins. The Basic Local Alignment Search Tool allows for various types of searches, and its scoring system and E-values help determine the significance of the sequence alignments. This powerful tool aids researchers in understanding novel genes, grouping them into families, and uncovering essential information for functional and structural analysis of unknown sequences.

Step-by-step solution

1. Definition of BLAST

BLAST, which stands for Basic Local Alignment Search Tool, is a widely used algorithm that allows the comparison of a query sequence (DNA or protein) against a database of target sequences to find regions of local similarity. The primary purpose of BLAST is to identify homologous sequences, infer function, and detect conserved domains in the sequences.

2. Basic features of BLAST

There are several features to consider when using BLAST, including different types of BLAST searches, the scoring system for aligning, E-values, and sequence databases. The most common types of searches include: 1. Blastp: compares protein sequences 2. Blastn: compares nucleotide sequences 3. Blastx: compares a nucleotide sequence translated in all six possible frames to protein sequences 4. tBlastn: compares a protein sequence to translated nucleotide sequences 5. tBlastx: compares translated nucleotide sequences to other translated nucleotide sequences The scoring system determines the degree of match between two sequences, and the E-value provides the expectations of how likely the alignment occurs by chance. The lower the E-value, the higher the statistical significance of the match.

3. Importance of BLAST in analyzing gene and protein sequences

BLAST plays a crucial role in research as it helps researchers identify sequences that share similarities with the query sequence, which in turn can help determine the function of the sequence, its possible structure, and evolutionary relationships. Thus, it helps in predicting novel functions in uncharacterized genes, grouping genes into families, and identifying conserved domains needed for specific biological functions.

4. Example of BLAST search

For example, we want to analyze the function of an unknown protein sequence. We perform a Blastp search, where we compare the query protein sequence against the protein database. After running the search, we might find several homologous sequences with known functions and structures. Based on these homologous sequences, we can infer that our query protein is likely to have a similar function and structure. Additionally, we might learn the evolutionary relationships between the query protein and other sequences in the database. This information can help steer our research toward understanding the biological roles and applications of the unknown protein sequence.