BBAU LUCKNOWA Presentation

On

By

Rishabh Garg(M.Sc. IM 1st sem.)

Submitted to:

Dr. V. Mishra

SEQUENCE ANALYSIS

Defining Sequence Analysis• Sequence Analysis is the process of subjecting

a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution.

• It includes- Sequencing: Sequence Assembly ANALYSIS

Alignment: Searching (in Databases)

APPLICATIONS (Uses)• The comparison of sequences in order to find similarity,

often to infer if they are related (homologous).• Identification of intrinsic features of the sequence such

as active sites, post translational modification sites, gene-structures, distributions of introns and exons.

• Identification of sequence differences and variations such as point mutations and single nucleotide polymorphism (SNP) in order to get the genetic marker.

• Revealing the evolution and genetic diversity of sequences and organisms

• Identification of molecular structure from sequence alone.

• Genetic diseases

DNA SEQUENCING• DNA sequencing is the process of determining the

precise order of nucleotides or order of the four bases—adenine, guanine, cytosine, and thymine, in a strand of DNA.

• Expressed Sequence Tag (EST) is a short sub-sequence of a cDNA sequence. ESTs may be used to identify gene transcripts, and are instrumental in gene discovery and in gene-sequence determination.

• Methods: Sanger Sequencing or Chain Termination

Method Pyrosequencing Shotgun Sequencing method

Fluorescence-Based Sequencing 

SEPERATED

NUCLEOTIDE

SEQUENCES

INDIVIDUAL

PEAKS

CHROMATOGRAPH

Protein Sequencing• Protein sequencing is a technique to

determine the amino acid sequence of a protein, as well as which conformation the protein adopts and the extent to which it is complexed with any non-peptide molecules.

• Methods:Edman DegradationMass Spectroscopy

• Mass spectrometry (MS) is an analytical technique that ionizes chemical species and sorts the ions based on their mass to charge ratio.

Sequence Assembly• Sequence assembly refers to the

reconstruction of a DNA sequence by aligning and merging small DNA fragments. It is an integral part of modern DNA sequencing.

(1) cutting the DNA into small pieces,

(2) reading the small fragments,

(3) reconstituting the original DNA by merging the

information on various fragment.

Sequence Alignment• Sequence Alignment is a way of arranging the

sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.

• It involves the identification of the correct location of deletions and insertions that have occurred in either of the two lineages since the divergence from a common ancestor.

TYPES• On the basis of number of comparing

sequencing strand, it is of two types:

Pair-wise Alignment

Multiple Sequence Alignment

Pair-wise Sequence Alignment• Pair-wise sequence alignment only compares two

sequences at a time.• Optimality is based on SCORE.A pairwise alignment consists of a series of paired

bases, one base from each sequence. There are three types of pairs:

(1) matches = the same nucleotide appears in both sequences. (2) mismatches = different nucleotides are found in the two sequences. (3) gaps = a base in one sequence and a null base in the other.

• Algorithm used are Needleman-Wunsch algorithm and the Smith-Waterman algorithm

BLAST (Basic Local Alignment Search TooL)

Multiple Sequence Alignment• Multiple sequence alignment (MSA) is a sequence

alignment of three or more biological sequences, generally protein, DNA, or RNA.

ClustalW, PROBCONS, MUSCLE

DATABASES• Biological databases are libraries of life

sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis.

UniGene is an NCBI database of the TRANCRIPTOME

DNA Data Bank of Japan (DDBJ) European Bioinformatics Institute (EMBL-EBI) SWISS-PROT &Tr-EMBL

THANKYOU!