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BBAU LUCKNOW
A Presentation
On
By
PRASHANT TRIPATHI
(M.Sc. IM)
BBAU
SEQUENCE ANALYSIS
Defining Sequence Analysis
• Sequence Analysis is the process of
subjecting a DNA, RNA or peptide sequence to
any of a wid...
APPLICATIONS (Uses)
• The comparison of sequences in order to find
similarity, often to infer if they are related
(homolog...
DNA SEQUENCING
• DNA sequencing is the process of determining
the precise order of nucleotides or order of the
four bases—...
Fluorescence-Based
Sequencing
SEP
ER
ATE
D
NU
CLE
OTI
DE
SE
QU
EN
CES
I
N
D
I
V
I
D
U
A
L
P
E
A
K
S
CHROMATOGRAPH
Protein Sequencing
• Protein sequencing is a technique to
determine the amino acid sequence of
a protein, as well as which...
• Mass spectrometry(MS) is an analytical technique that
ionizes chemical species and sorts the ions based on their mass
to...
Sequence Assembly
• Sequence assembly refers to the
reconstruction of a DNA sequence
by aligning and merging small DNA fra...
Sequence Alignment
• Sequence Alignment is a way of arranging the
sequences of DNA, RNA, or protein to identify
regions of...
TYPES
• On the basis of number of comparing
sequencing strand, it is of two types:
 Pair-wise Alignment
Multiple Sequenc...
Pair-wise Sequence Alignment
• Pair-wise sequence alignment only compares
two sequences at a time.
• Optimality is based o...
• 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
sequen...
DATABASES
• Biological databases are libraries of life
sciences information, collected from scientific
experiments, publis...
THANKYOU!
SEQUENCE ANALYSIS
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SEQUENCE ANALYSIS

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SEQUENCE ANALYSIS

  1. 1. BBAU LUCKNOW A Presentation On By PRASHANT TRIPATHI (M.Sc. IM) BBAU SEQUENCE ANALYSIS
  2. 2. 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)
  3. 3. 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
  4. 4. 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
  5. 5. Fluorescence-Based Sequencing SEP ER ATE D NU CLE OTI DE SE QU EN CES I N D I V I D U A L P E A K S CHROMATOGRAPH
  6. 6. 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 Degradation Mass Spectroscopy
  7. 7. • Mass spectrometry(MS) is an analytical technique that ionizes chemical species and sorts the ions based on their mass to charge ratio.
  8. 8. 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.
  9. 9. 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.
  10. 10. TYPES • On the basis of number of comparing sequencing strand, it is of two types:  Pair-wise Alignment Multiple Sequence Alignment
  11. 11. 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.
  12. 12. • Algorithm used are Needleman-Wunsch algorithm and the Smith-Waterman algorithm BLAST (Basic Local Alignment Search TooL)
  13. 13. 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
  14. 14. 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
  15. 15. THANKYOU!

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