Multiple Sequence Alignment Tool Using NCBI COBALT

Multiple Sequence Alignment Tool Using NCBI COBALT

1. MSAT
MULTIPLE SEQUENCE ALIGNMENT TOOL
BY
GROUP 2
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2. OVERVIEW
Sequencealignment
Typesofsequencealignments
Multiplesequencealignment
PurposeofMSA
TypesofMSA
Progressivealignment
Pros & Cons
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3. SEQUENCEALIGNMENT
Inbioinformatics,asequencealignmentsawayofarrangingthesequencesofDNA,RNA
,orproteintoidentifyregionsofsimilaritythatmaybeaconsequenceoffunctional,stru
ctural,orevolutionaryrelationshipsbetweenthesequences.
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4. SEQUENCE ALIGNMENT
SEQUENCEALIGNMENT Sequences oftencontainhighlyconservedregions
Theseregionscanbeusedforinitialalignments
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5. TYPESOFSEQUENCEALIGNMENTS
Pair‐wisealignment
Dotmatrixmethod
Dynamicprogramming
Wordmethods
Multiplesequencealignment
Dynamicprogramming
Progressivemethods
Iterativemethods 2/22/2018
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6. MULTIPLESEQUENCEALIGNMENT
Amultiplesequencealignmentis tool that simultaneously aligns multiple protein
sequences, automatically utilizes information about protein domains, and has a good
compromise between speed and accuracy will have practical advantages over
current tools
Theprincipleisthatmultiplealignmentsareachievedbysuccessiveapplicationofp
airwise methods.
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7. PURPOSEOFMSA
Inordertocharacterizeproteinfamilies,identifysharedregionsofhomologyina
multiplesequencealignment
Determinationoftheconsensussequenceofseveralalignedsequences.
Consensussequencescanhelptodevelopasequence“fingerprint”whichallo
wstheidentificationofmembersofdistantlyrelatedproteinfamily(motifs)
MSAcanhelpustorevealbiologicalfacts
aboutproteins,likeanalysisofthesecondary/tertiarystructure
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9. TYPESOFMSA
Dynamicprogrammingapproach
Computesanoptimalalignmentforagivenscorefunction.Becauseofitshighru
nningtime,itisnottypicallyusedinpractice.
Progressivemethod
Thisapproachrepeatedlyalignstwosequences,twoalignments,orasequence
withanalignment.
Iterativemethod
Workssimilarlytoprogressivemethodsbutrepeatedlyrealignstheinitialsequence
saswellasaddingnewsequencestothegrowingMSA.
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10. PROGRESSIVEALIGNMENT
Themostwidelyusedapproach
BuildsupafinalMSAbycombiningpairwise
alignmentsbeginningwiththemostsimilarpairandprogressingtothemostdistantlyr
elated
Progressivealignmentmethodsrequiretwostages:
First stageinwhichtherelationshipsbetweenthesequencesarerepresentedasatree,
calledaguide tree
‐SecondstepinwhichtheMSAisbuiltbyadding
thesequencessequentiallytothegrowingMSA accordingtotheguidetree
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11. USING COBALT NCBI
Constraint based alignment tool that implements a general framework for
multiple alignment of protein sequences
COBALT finds a collection of pairwise constraints derived from database
searches, sequence similarity and user input, combines these pairwise
constraints, and then incorporates them into a progressive multiple
alignment
COBALT has reasonable runtime performance and alignment accuracy
comparable to or exceeding that of other tools for a broad range of
problems
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12. USING COBALT NCBI
COBALT has a general framework that uses progressive multiple alignment
to combine pairwise constraints from different sources into a multiple
alignment
When the same domain matches to multiple sequences, we can infer
several potential pairwise constraints based on these domain matches
CDD ( Conserved Domains Database ) also contains auxiliary information
that allows COBALT to create partial profiles for input sequences before
progressive alignment begins, and this avoids computationally expensive
procedures for building profiles
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13. RUNTIME OF COBALT
The runtime performance of COBALT is highly data driven
COBALT is about five times faster than ProbCons
COBALT is included in the NCBI C++ Toolkit
Numerous auxiliary programs were written in C, C++ and Perl to automate
testing and summarize results
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14. AVAILABILITY
COBALT is included in the NCBI C++ toolkit. A Linux executable for COBALT,
and CDD and PROSITE data used is available at:
https://www.ncbi.nlm.nih.gov/tools/cobalt/re_cobalt.cgi
Contact: [email protected]
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15. STEP 1
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Go to https://www.ncbi.nlm.nih.gov/

16. STEP 2
The Swiss-Protprotein sequence for Schizosaccharomycespombe Clr4 is
O60016.2.
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17. STEP 3
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18. Step 4
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19. STEP 5
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20. STEP 6
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21. Your patience is greatly appreciated….
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22. RESULT
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23. STEP 6
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Select First 11

24. STEP 7
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25. Your patience is greatly appreciated….
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26. RESULTS
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27. RESULTS
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28. STEP 8
Notice that the above multiple alignment cant be edited “Edit and
Resubmit” link at the top of the COBALT results to remove the undesired
protein than search again.
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29. STEP 8 (a)
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30. STEP 8 (b)
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31. PROS AND CONS OF PROGRESSIVE
METHOD OF ALIGNMENT
PROS:
Efficient enough to implement on a large scale for
many (100s to 1000s) sequences.
Progressive alignment services are commonly available
on publicly accessible web servers, so users need not
locally install the applications of interest.
Most widely used method of multiple sequence
alignment because of speed and accuracy.
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32. CONS…….
Progressive alignments are not guaranteed to be
globally optimal.
The primary problem is that when errors are made at
any stage in growing the MSA, these errors are then
propagated through to the final result.
Performance is also particularly bad when all of the
sequences in the set are rather distantly related
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33. REFERENCES
https://insidescienceresources.wordpress.com/2017/05/15/ncbi-
bioinformatics-tools-protein-blast-cobalt-and-cn3d-structure-viewer/
https://academic.oup.com/bioinformatics/article/23/9/1073/272774
https://www.ncbi.nlm.nih.gov/
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