Scribd
Upload
24 views26 pages

Blast

Uploaded by

Sarib Shahid
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
24 views26 pages

Blast

Uploaded by

Sarib Shahid
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
You are on page 1/ 26

DNA/Protein sequence analysis tools

Dr. Farrukh Azeem


Department of Bioinformatics & Biotechnology
Government College University Faisalabad
(www.gcuf.edu.pk)
Basic Local Alignment Search Tool
(BLAST) Altschul 1990

• BLAST finds regions of similarity between biological sequences. The


program compares nucleotide or protein sequences to sequence
databases and calculates the statistical significance.
Database Similarity Searching
Different variants and programs used in NCBI-BLAST
Protein BLAST

Protein BLAST
Example- General BLAST against all genomes
Where does the score (S) come from?
• The quality of each pair-wise alignment is represented
as a score and the scores are ranked.
• Scoring matrices are used to calculate the score of the
alignment base by base (DNA) or amino acid by amino
acid (protein).
• The alignment score will be the sum of the scores for
each position.

BLOSUM 45 BLOSUM 62 BLOSUM 90


PAM 250 PAM 160 PAM 100
More Divergent Less Divergent

PAM …… more evolutionary meaning


BLOSUM…. More empirical basis
13
E-values
The significance of each alignment is computed as an E value (E).
Expectation value. The number of different alignments with scores
equivalent to or better than S that are expected to occur in a database
search by chance. The lower the E value, the more significant the score.

E<1e-50 or 1x10-50 …………….. Database match is a result of homologous match

E is between 0.01 and 1e-50 …………….. Database match can be considered a homologous match

E is between 0.01 and 10 …………….. Database match is non- significant but additional information

E>10 …………….. Database match is unrelated or fall below the detection limit of this method
Example- Organism specific BLASTN
Example- Organism specific BLASTX

You might also like