HOA1&2 - Module 3 - PREHISTORCI ARCHITECTURE OF KERALA.pptx
BIOINFO.pptx
1. Synopsis presentation
on
Tools for comparative genomics: BLAST2, Vista, MUMmer,
COG, VOG
Presented by:
Mubeena H (1AY20BT020)
Prakruthi (1AY20BT023)
Prastuthi Elish (1AY20BT024)
Vaishnavi P(1AY20BT030)
DEPARTMENT OF BIOTECHNOLOGY ENGINEERING
ACHARYA INSTITUTE OF TECHNOLOGY
(Affiliated to Visvesvaraya Technological University, Belagavi, Recognized by AICTE and Accredited by NBA, New Delhi)
Under the Guidance of :
Pruthvish R
2022-23
3. INTRODUCTION
● Large dataset for orthologous-sequence comparisons.
● Based on the observation
● Studying evolutionarily conserved sequences is a reliable strategy to uncover regions of the human
genome with biological activity.
● These new publicly accessible resources have been successfully exploited by investigators for the
discovery of biomedically important new genes and sequences involved in gene regulation.
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4. BLAST2
● BLAST is a rapid sequence comparison tool
● Much faster than dynamic programming methods
● A number of important scientific contexts
● Finds multiple local alignments
● Convenient strategy to study the genome variations
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5. Clicking the BLAST2 link will bring you to the BLAST2 page, which looks like this:
● blastp
● blastn
● Generates a gapped alignment
● Different scoring matrices
● Changing gap existence
● Assess a score (a+bk)
● Default values
● Incorrect parameter setting
● Compositional complexity
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6. The results page will look like this
● The graph is a dot plot
● Shows the user visually how the
entirety of the two strands aligned.
● The light blue line in the top left
corner indicate an inverted repeat
● Each alignment is evaluated
separately.
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7. MUMmer
• MUMmer is bioinformatics software system for sequence alignment.
• MUMmmer is based on the suffix tree algorithm .
• The acronym "MUMmer" comes from "Maximal Unique Matches", or MUMs.
• The MUMmer software is open source and can be found at the MUMmer home page.
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12. VISTA
INTRODUCTION
● In order to increase number of available DNA sequences from multiple species, the need for comparative
genomics tools to functionally annotate the sequences is needed.
● VISTA family of tools is based on global alignment strategies
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13. TYPES OF VISTA
There are three VISTA servers:
● 1. Genome VISTA
● 2. m VISTA
● 3.rVISTA
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14. VISUALISATION OF ALIGNED GENOME SEQUENCE
There are two schemes of visual data presentation
● VISTA browser — VISTA Browser is a Java program which is very efficient for interactively visualizing.
● VISTA track– accessible through vista browser, displays results of comparative analysis.
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15. PROCEDURE TO USE VISTA
● A sequence up to 300 kb long can be submitted
● the user immediately receives a link
● conservation can be viewed using VISTA Browser and Text Browser.
● results for all alignments are provided to the user in Text Browser.
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16. APPLICATIONS
● Investigate the pre calculated alignments.
● To perform pairwise alignments of DNA
● Speed and accuracy in detecting homologies.
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17. COG
● COG stands for Cluster of orthologous genes.
● COG is defined as three or more proteins from the genomes of distant species that are more
similar to each other than to any other protein within the individual genome.
● COGS can be used to predict the function of homologous proteins.
● Important in comparative genomics studies
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19. APPLICATION OF COG
● Predicts functions of individual proteins
● Important in comparative genomic studies
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20. VOG
● VOG indicates viral orthologous groups
● Helps to study genomic sequences in viruses
● Previous versions of pVOG’s have been described under POG(phage orthologous groups).
● The function of VOG has changed from assessing domain-based orthologous assignments to full
length proteins.
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24. Applications
● To understand the history of viral protein families
● To aid in evolutionary classification of known phages
● To identify virus-specific genes that could be used as diagnostic markers of
prokaryotic viruses presence in a given environment
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