Sequence Analysis

Sequence analysis is the use of various bioinformatics methods and tools to determine the biological function and/or structure of genes and the proteins they code for.

Sequence Analysis Techniques

How to perform Sequence Analysis?

To perform Sequence Similarity Search we use NCBI BLAST.

What is NCBI BLAST?
NCBI's BLAST, is used to compare the sequence of a particular gene or protein with other sequences from a variety of organisms.

What is BLAST?
BLAST (Basic Local Alignment Search Tool) is a set of programs designed to perform similarity searches on all available sequence data. We can use this searches to gain insight into the function and biological importance of gene products.

BLAST uses an algorithm developed by NCBI that seeks local alignment (the alignment of some portion of two sequences) as opposed to global alignment (the alignment of two sequences over their entire length). By searching for local alignments, BLAST is able to identify regions of similarity within two sequences.

Services provided by BLAST :

blastp - comparing an amino acid query sequence with others stored in protein sequence databases
blastn - comparing a nucleotide query sequence against a nucleotide sequence database
blastx - comparing a nucleotide query sequence translated in all reading frames with other amino acid sequences stored in protein sequence databases

To proceed with the BLAST we need the FASTA formatted Amino acid sequence.

How to obtain a FASTA Formatted Sequence?

Go to NCBI Home page.
Enter the Search option (eg: protien, Genome, etc) for any particular organism (eg: human, rat etc) and in the display option select FASTA.
Then click Go.
The FASTA sequence starts with > symbol.
eg: >gi|73535847|pdb|1Z9O|C Chain C, 1.9 Angstrom Crystal Structure Of The Rat Vap-A Msp Homology Domain In Complex With The Rat Orp1 Ffat Motif
GSHMAKHEQILVLDPPSDLKFKGPFTDVVTTNLKLQNPSDRKVCFKVKTTAPRRYCVRPNSGVIDPGSIV
TVSVMLQPFDYDPNEKSKHKFMVQTIFAPPNISDMEAVWKEAKPDELMDSKLRCVFEM

Copy the sequence.
From the home page click BLAST. Then you need to select the BLAST service you need to use like blastp, blastn etc.
Paste the sequence in the form.
Click on the BLAST button.

Analyse the result.