alignment search tool

1. fasta
M.Ummul halilunnisa
M.Sc –Ist year
Pondicherry university.

2. Introduction:
-fasta was developed by Lipman and pearson in 1985.
-tool used align the sequences(protein & DNA)
-best to make protein protein comparison.
-blast (modified version)

3. Fasta = protein to protein
Tfasta = protein to DNA
Lfasta = identifies 1/more regions of similarity
Plfasta= presents a dot matrix plot of regions of sequence
similarity between 2 sequences
Expansions:

6. Derived from logic of the dot plot
 compute best diagonals from all frames of alignment
The method looks for exact matches between
words in query and test sequence
 DNA words are usually 6 nucleotides long
 protein words are 2 amino acids long
Idea ?

7. Howto do the sequence alignment usingfasta?
 Identify the common k-words between the sequences.
 Identify the best diagonals.
 Score the regions.
 Join the aligned regions.
 Optimal alignment.

8. 1.Identify the common k words:
-word based search=k tups
-local alignment
-finds the matching words
-creates diagonal by dot plot

10. 2.Identify the best diagonals:

11. Scoretheregions:
 Score the best regions using =init 1
 It tries to join high scoring diagonals
 Rescoring by PAM-250 matrix =init n

12. Jointhe alignedregions& make an optimal alignment:

13. Howto manuallydo the fastasearch?
Retrieve the
sequence
from uniprot
paste the
sequence in
fasta tool
Submit the
sequence

20. Blast vs Fasta
• Blast is much faster than Fasta.
• Blast is much more accurate than Fasta.
• For closely matched sequences Blast is very accurate and for dissimilar sequence Fasta
is better software.
• Blast can be modified according to the need but Fasta cannot be modified.
• Blast has to use Fasta input format to get the output data.
• Blast is much more versatile and widely used than Fasta.