Sequence similarity tools

1. Sequence Similarity tools
Smt.P.Sangeetha,
Lec. In Biotechnology,
KVRGCW(A),Kurnool

2. BLAST[Basic Local Alignment Search Tool]
 BLAST algorithm was described by Altschul et al in 1990.
BLAST is a set of similarity search programs designed to explore all of the available sequence
databases regardless of whether the query is protein or DNA.
 BLAST is a pairwise sequence homology search tool that finds both locally and globally
alignable sequences.
BLAST allows to take a newly derived sequence from the gene of interest and search for any
other similar sequences - a “match” or a “hit” which gives valuable information about the
biological function of the gene of interest.

3. BLAST
 BLAST calculates all segment pairs( a pair of sub sequences of same length that form an
ungapped alignment) between query and the database sequences, above a scoring threshold.
 The algorithm searches for fixed length hits, which are then extended until certain
threshold parameters are achieved.
 The resulting High Scoring Pairs (HSP) form the basis of the ungapped alignments that
characterise BLAST output.

4. BLAST Programs
◦ BLAST n : To find nucleotide sequences similar to query sequence.
◦ MEGABLAST : A rapid method developed form comparing groups of similar sequences.
◦ BLAST P : To find the protein sequences similar to the query sequence.
◦ BLAST X : To find similar proteins to the translated query sequence.
◦ PSI BLAST : To search short conserved sequences.
◦ t BLAST n : To find similar proteins in a translated nucleotide database.
◦ t BLAST x : To find similar proteins to translated query in a protein database.

5. Features of BLAST
 Sequence similarity tool.
 It compares a sequence with another sequence in the databases.
 It calculates the sequence similarity.
 It is a pairwise sequence homology search tool that finds both globally and locally alignable
sequences.

6. BLAST Output

7. Interpretation of BLAST Output
 Red, pink and green matches are good hits.
 Black is a bad hit.
 Bit score : It is the measure of statistical significance of the
alignment.

8. FASTA
 The FASTA algorithm was described by Lipman and Pearson in 1985. FASTA pronounced as
FAST- Aye denotes it is FAST Alignment.
 FASTA is used for a fast protein comparison or a fast nucleotide comparison.
 This program achieves a high level of sensitivity for similarity searching at high speed.
 The FASTA program is much more sensitive than BLAST programs, which is reflected by the
length of time to produce results.
The FASTA produces local alignment scores for the comparison of the query sequence to
every sequence in the database.

9. Features of FASTA
 Sequence analysis tool.
FASTA means FASTA All for a fast protein or nucleotide comparison.
The parameter in FASTA is k-tuple.
The default matrix for BLAST/ FASTA is BLOSUM62
Gap penalties : Gap open penalty : Penalty for 1st residue in a gap. (-12 for proteins, -16 for
DNA) and Gap Extension Penalty : Penalty for additional residues in a gap. (-2 for proteins, -
4 for DNA)
 FASTA is slower than BLAST but more accurate when making comparison.

10. CLUSTAL
CLUSTAL W –
Online tool
CLUSTAL X –
Offline tool

11. CLUSTAL W
 CLUSTAL W is a general purpose multiple sequence alignment program for DNA or protein.
 It produces meaningful multiple sequence alignments of divergent sequences.
 It calculates the best match for the selected sequences, and lines them up so that the
identities, similarities and differences can be seen.
Evolutionary relationships can be seen via viewing Cladograms and Phylograms.

12. CLUSTAL W
 CLUSTAL W is a fully automatic program for global multiple alignment of DNA and protein
sequences.
 Sequences can be aligned across their entire length (global alignment) or in certain regions
(local alignment).
 Global alignments need to use gaps while local alignments can avoid them, aligning regions
between gaps.

13. You
Thank