Question

How do the smith waterman and BLAST algorithm differ in terms of optimality of results and computational resources required to produce them?

Answer 1

BLAST - BASIC LOACL ALIGNMENT SEARCH TOOL

IS AN ALGORITHM/PROGRAM FOR COMPARISON OF BASIC BIOLOGICAL INFORMATION. IT USES THE AMINOACID SEQUENCES (IN CASE OF PROTEINS) AND NUCLEOTIDE SEQUENCES(IN CASE OF DNA AND RNA). HERE WE COMPARE OUR SEQUENCE OF INTEREST WITH A DATABASE OF SEQUENCES.

RESULT/OUTPUT USING BLAST - 1. FAST (THAN SMITH WATERMANN)

2. DOES NOT GUARANTEE OPTIMAL ALIGNMENT OF THE QUERY SEQUENCE WITH THE DATABASE.

3. TIME-SAVING AS IT TAKES INTO ACCOUNT MORE SIGNIFICANT PATTERNS.

COMPUTATIONAL RESOURCES FOR BLAST PROGRAM

STEP 1 - SELECTION OF BLAST PROGRAM - CHOSE AMONGST HE  VARIOUS DIFFERENT BLAST PROGRAMS LISTED - Blastp, Blastn, Blastx, tBlastn, tBlastx

STEP 2 - Enter/Upload the query sequence - Enter a query sequence by pasting the sequence in the query box or upload it in FASTA format.

STEP 3 - Selection of Database

STEP 4 - Selection of Algorithm and its Parameters

DIFFERENT ALGORITHMS

i. Nucleotide BLAST algorithm - a. MegaBLAST - FOR HIGHLY SIMILAR SEQUENCES

b. discontinuous MegaBLAST - FOR MORE DISSIMILAR SEQUENCES

c. BLASTn - FOR SOMEWHAT SIMILAR SEQUENCES

ii. Protein BLAST algorithms - a. Blastp- protein-protein BLAST

b. PSI - BLAST POSITRON SPECIFIC ITERATED BLAST

c. PHI - BLAST PATTERN HIT INITIATED BLAST

d. DELTA - BLAST PATTERN HIT INITIATED BLAST

DIFFERENT ALGORITHMIC PATTERS

TARGET SEQUENCES, SHORT QUERIES, E-VALUES, WORD SIZE, QUERY RANGE, SCORING PARAMETERS(MATCH/MISMATCH SCORES) AND GAP PENALTIES

STEP 5 - RUN THE BLAST PROGRAM.

SMITH WATERMAN ALGORITHM - LOOKS FOR OPTIMAL LOCAL ALIGNMENT BETWEEN TWO AMINOACID SEQUENCES/NUCLEOTIDE SEQUENCES.THE BASIC WORKING OF THIS ALGORITHM IS SIMILAR TO THAT OF NEEDLEMAN WUNCH ALGORITHM.

WORKING - 1. MATRIX INITIALIZATION - THIS INCLUDES DETERMINING THE SUBSTITUTION MATRIX AND THE GAP PENALTY SCHEME

2. FILLING MATRIX WITH APPROPRIATE SCORES

3. TRACING BACK SEQUENCES FOR AN OPTIMAL ALIGNMENT.

RESULT/OUTPUT USING SMITH WATERMAN -  1. IDENTIFIES OPTIMAL LOCAL ALIGNMENT

2. PRECISE

3. SENSITIVE

4. TIME-CONSUMING

5. COMPUTER POWER INTENSIVE