Answer to Question #154939 in Bioinformatics for vaibhav

Question

(a) BLAST

What is the impact on

• the speed of the heuristic

• the number of false negatives

• the number of false positives

of the following changes in BLAST parameters:-

(i) increase/decrease in w; where w is the length of words

(ii) increase/decrease T; where T is the least score to find list of words corresponding to each word from query sequence when scored using a pair-score matrix.

(iii) increase/decrease in S; where S is the threshold score after extension of alignment

(b) The higher the level of accuracy required in DNA sequences, more time consuming the process of database formation is. What is done to reduce this time? Does this bring in errors? Mention how accuracy is then improved.

Answer 1

Number of words in the list depends on w and

T, and is much less than 20cubed.

increase/decrease in w will increase/decrease heuristic, false negatives and false positive respectively.

increase/decrease T will increase/decrease heuristic, false negatives and false positive respectively.

increase/decrease in S will increase/decrease heuristic, false negatives and false positive respectively.

High-throughput sequencing, which includes next-generation "short-read" and third-generation "long-read" sequencing methods,[nt 1] applies to exome sequencing, genome sequencing, genome resequencing, transcriptome profiling (RNA-Seq), DNA-protein interactions (ChIP-sequencing), and epigenome characterization. Resequencing is necessary, because the genome of a single individual of a species will not indicate all of the genome variations among other individuals of the same species.