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Sequence Alignment

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6 views18 pages

Sequence Alignment

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my jw
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Sequence Alignment

Nilakshi Samaranayake
Terminology
 Homolog
– A gene related to a second gene by descent

 Paralog
– Paralogs are genes related by duplication within a
genome
 Ortholog
– Orthologs are genes in different species that evolved
from a common ancestral gene by speciation

Orthologs retain the same function in the course of


evolution, whereas paralogs evolve new functions
Orthology
What is sequence alignment?

 Procedure of comparing two or more


sequences by looking for a series of
individual characters or character patterns
that are in the same order in the sequences.
Alignment methods

 Global alignment
– create an end-to-end alignment of the
sequences to be aligned.
– alignment is carried out from beginning till end
of the sequence to find out the best possible
alignment
Alignment methods

 Local alignment
– find one, or more, alignments describing the most
similar region(s) within the sequences to be
aligned
– alignment tends to stop at the ends of regions of
identity or strong similarity
Alignment methods

 Dynamic programming
– Needleman-Wunsch algorithm
– Smith-Waterman algorithm
 Eg: EMBOSS
 Alternative methods (eg: probabilistic
methods)
– EMBL FASTA
(http://fasta.bioch.virginia.edu/fasta_www2/fasta_l
ist2.shtml)
– NCBI BLAST
Pairwise sequence alignment

 To find the best-matching piecewise (local) or


global alignments of two query sequences.
 Used to identify regions of similarity that may
indicate functional, structural and/or
evolutionary relationships between two
biological sequences (protein or nucleic
acid).
Eg: EMBOSS
Multiple sequence alignment

 Extension of pair wise alignment to


incorporate more than two sequences at a
time
Eg: Clustal Omega
Cobalt
Structural alignment
Scoring and Alignment Representation
Scoring and Alignment Representation
Applications in genomics?
Alignment Software
 EMBOSS
http://www.ebi.ac.uk/Tools/psa/emboss_water/nucleotide
.html
 Clustal Omega
http://www.ebi.ac.uk/Tools/services/web/toolform.ebi?tool
=clustalo
 MUSCLE
http://www.ebi.ac.uk/Tools/msa/muscle/
 BLAST
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE
_TYPE=BlastHome

Refer algorithms used in the different software above


Exercise 1

https://www.ncbi.nlm.nih.gov/search/

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