2. what is the blast effect course hero

How does a blast algorithm work?

What is a blast sequence?

What is the difference between blast and fasta?

What is a nucleotide blast?

What is reverse position specific blast?

What is PSI blast?

What is the target of tblastn?

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How does a blast algorithm work?

BLAST is a heuristic method which means that it is a dynamic programming algorithm that is faster, efficient but relatively less sensitive. For BLAST (ing) any sequence, there is a query sequence and a target sequence/database.

What is a blast sequence?

The query sequence is the sequence for which we want to find out the similarity and the target sequence is a sequence/database against which the query sequence is aligned. Blast returns the output in the form of hit tables that are arranged in decreasing order of matched accession number along with their titles, query coverage, sequence identity, score, and an e-value in separate columns. The reliability of the matched sequences is assessed by e-value.

What is the difference between blast and fasta?

Blast is a greedy algorithm that was developed by Altschul et al. [1]. It is similar to FASTA but more efficient. As FASTA uses a ktup parameter, similarly BLAST also uses a window size for proteins and nucleotides. Both assume that good alignments contain short stretches of exact matches. BLAST is an improvisation over FASTA in the sense that it is faster, more sensitive, more statistically significant, and easy to use. There is a threshold in blast known as ‘Minimal Score denoted as ‘ S ’. It means that whatever the match is between the query and the database is it must have a value equal to or greater than S.

What is a nucleotide blast?

It is a type of blast in which the nucleotide sequence is against the nucleotide database but at the protein level. In other words, the nucleotide query sequence and the target sequences are both translated into their corresponding protein sequences and then aligned together. Both the query and the target are translated in all 6 reading frames.

What is reverse position specific blast?

Reverse Position Specific (RPS) Blast is also similar to PSI Blast which matches the query with a set of conserved domain, HMM profiles, or pre-aligned profiles. In this kind of blast, the query sequence (DNA / protein) is searched against an existing collection of conserved domains, a preconfigured MSA of various genes.

What is PSI blast?

Position-Specific Iterated (PSI) Blast is very sensitive and usually used for protein similarity search. The query sequence is taken and subjected to blastp which results in the formation of a multiple sequence alignment (MSA) of most similar sequences. From this MSA, the pattern that identifies the query and its homologs are taken, then this conserved pattern is subjected to blastp again to filter the database. This process of identifying patterns from MSA, blasting the pattern against the database again creating MSA, and then again identifying a redefined pattern is PSI Blast.

What is the target of tblastn?

In tblastn, the query is a protein and the target is a nucleotide sequence/database. Here, the protein sequence is searched against a nucleotide database which is translated to its corresponding proteins.

What is the blast effect?

2. What is the blast effect? The blast effect is the outward rush of gasses from the point of origin of the bomb, it can be over 7000 miles per hour or 3129.28 meters/s. It is related to Newton’s second law because the second law states that the acceleration of an object depends on the net force acting on it.

How is evidence from a fire scene collected?

How is the evidence from a fire scene collected? What should be avoided? Evidence from a fire scene is collected by being placed in an air-tight container to prevent the evaporation of flammable liquids. Glass cases as well as clean paint cans with airtight lids. Plastic bags should be avoided because they can produce dangerous gases when they are mixed with flammable liquids. Crit thinking q’s

What are the two types of explosives?

3. What are the two types of high explosives? The two types of high explosives are primary and secondary. The difference is very slight, primary explosives are easily detonated and are very sensitive to heat and friction, secondary explosives, like tnt or dynamite, are less sensitive to heat and friction. Primary explosives are usually not used in homemade bombs, because of their volatile nature.

How are fire scenes different from regular crime scenes?

How are fire scenes different than regular crime scenes for investigators? Fire scenes are different than regular crime scenes because the evidence that was at the scene of the crime is most likely burned and destroyed, also the individual who committed the crime is not at the crime scene usually. This makes it hard to piece together who did it or why. You will also at the same time have to use a different type of evidence to piece together the crime, instead of the evidence at the scene of the crime.

What is substrate control?

4. What is a substrate control? Why is it done? Substrate control is an uncontaminated sample of a flammable liquid. It allows Forensic scientists to compare two samples to see whether a flammable liquid was present at the time.

How does a blast algorithm work?

BLAST is a heuristic method which means that it is a dynamic programming algorithm that is faster, efficient but relatively less sensitive. For BLAST (ing) any sequence, there is a query sequence and a target sequence/database.

What is a blast sequence?

The query sequence is the sequence for which we want to find out the similarity and the target sequence is a sequence/database against which the query sequence is aligned. Blast returns the output in the form of hit tables that are arranged in decreasing order of matched accession number along with their titles, query coverage, sequence identity, score, and an e-value in separate columns. The reliability of the matched sequences is assessed by e-value.

What is the difference between blast and fasta?

Blast is a greedy algorithm that was developed by Altschul et al. [1]. It is similar to FASTA but more efficient. As FASTA uses a ktup parameter, similarly BLAST also uses a window size for proteins and nucleotides. Both assume that good alignments contain short stretches of exact matches. BLAST is an improvisation over FASTA in the sense that it is faster, more sensitive, more statistically significant, and easy to use. There is a threshold in blast known as ‘Minimal Score denoted as ‘ S ’. It means that whatever the match is between the query and the database is it must have a value equal to or greater than S.

What is a nucleotide blast?

It is a type of blast in which the nucleotide sequence is against the nucleotide database but at the protein level. In other words, the nucleotide query sequence and the target sequences are both translated into their corresponding protein sequences and then aligned together. Both the query and the target are translated in all 6 reading frames.

What is reverse position specific blast?

Reverse Position Specific (RPS) Blast is also similar to PSI Blast which matches the query with a set of conserved domain, HMM profiles, or pre-aligned profiles. In this kind of blast, the query sequence (DNA / protein) is searched against an existing collection of conserved domains, a preconfigured MSA of various genes.

What is PSI blast?

Position-Specific Iterated (PSI) Blast is very sensitive and usually used for protein similarity search. The query sequence is taken and subjected to blastp which results in the formation of a multiple sequence alignment (MSA) of most similar sequences. From this MSA, the pattern that identifies the query and its homologs are taken, then this conserved pattern is subjected to blastp again to filter the database. This process of identifying patterns from MSA, blasting the pattern against the database again creating MSA, and then again identifying a redefined pattern is PSI Blast.

What is the target of tblastn?

In tblastn, the query is a protein and the target is a nucleotide sequence/database. Here, the protein sequence is searched against a nucleotide database which is translated to its corresponding proteins.