What is motif in protein sequence?

Protein sequence motifs are signatures of protein families and can often be used as tools for the prediction of protein function. A systematically derived motif database is therefore feasible, allowing the classification of the majority of the newly appearing protein sequences into known families.

What is a motif in DNA?

Sequence motifs are short, recurring patterns in DNA that are presumed to have a biological function. Often they indicate sequence-specific binding sites for proteins such as nucleases and transcription factors (TF).

What is a motif in protein?

Protein motifs are small regions of protein three-dimensional structure or amino acid sequence shared among different proteins. They are recognizable regions of protein structure that may (or may not) be defined by a unique chemical or biological function.

What does Phi blast do?

PHI-BLAST (Pattern-Hit Initiated BLAST) is a search program that combines matching of regular expressions with local alignments surrounding the match.

Why do motifs occur in DNA?

Do all proteins have motifs?

All proteins are made of basic secondary structure units, either α-helix or β-sheets, determined by hydrogen bonding between the amino acids within a peptide chain. On a larger scale, structures are formed by the combination of these secondary structures, and these can form supersecondary structures known as “motifs”.

What is difference between BLAST and FASTA?

The main difference between BLAST and FASTA is that BLAST is mostly involved in finding of ungapped, locally optimal sequence alignments whereas FASTA is involved in finding similarities between less similar sequences.

What is the difference between BLAST and Psi-Blast?

PSIBLAST uses position-specific scoring matrices (PSSMs) to score matches between query and database sequences, in contrast to BLAST which uses pre-defined scoring matrices such as BLOSUM62.

Is a domain a motif?

These consensus sequence patterns are termed motifs and domains. A motif is a short conserved sequence pattern associated with distinct functions of a protein or DNA. A domain is also a conserved sequence pattern, defined as an independent functional and structural unit. Domains are normally longer than motifs.

What is blast and how does it work?

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences…

How does blast calculate the significance of a match?

The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.

Why are blast designs important in bomb design?

Efficient blast designs combined with the proper choice of explosive can produce better fragmentation with associated lower operating costs compared to blast designs and explosives used under adverse conditions.

How does blast work to find local alignment?

Learn more. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.