Multiple Sequence Alignment Tool Using NCBI COBALT
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This document discusses multiple sequence alignment tools. It describes how multiple sequence alignments (MSAs) are used to identify conserved regions across related sequences and determine consensus sequences. The document outlines different types of MSA, including progressive and iterative methods. It also describes the steps to perform a multiple sequence alignment using COBALT at NCBI, including uploading sequences, running the alignment, and editing results. The progressive method is noted as the most widely used due to its speed and accuracy, though it may not produce globally optimal alignments.
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Multiple Sequence Alignment Tool Using NCBI COBALT
- 1. MSAT MULTIPLE SEQUENCE ALIGNMENT TOOL BY GROUP 2 2/22/2018 1
- 2. OVERVIEW Sequence alignment Types of sequence alignments Multiple sequence alignment Purpose of MSA Types of MSA Progressive alignment Pros & Cons 2/22/2018 2
- 3. SEQUENCE ALIGNMENT In bioinformatics, a sequence alignments a way of arranging the sequences of DNA, RNA , or protein to identify regions of similarity that may be a consequence of functional, stru ctural, or evolutionary relationships between the sequences. 2/22/2018 3
- 4. SEQUENCE ALIGNMENT SEQUENCE ALIGNMENT Sequences often contain highly conserved regions These regions can be used for initial alignments 2/22/2018 4
- 5. TYPES OF SEQUENCE ALIGNMENTS Pair‐wise alignment Dot matrix method Dynamic programming Word methods Multiple sequence alignment Dynamic programming Progressive methods Iterative methods 2/22/2018 5
- 6. MULTIPLE SEQUENCE ALIGNMENT A multiple sequence alignment is 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 The principle is that multiple alignments are achieved by successive application of p airwise methods. 2/22/2018 6
- 7. PURPOSE OF MSA In order to characterize protein families, identify shared regions of homology in a multiple sequence alignment Determination of the consensus sequence of several aligned sequences. Consensus sequences can help to develop a sequence “finger print” which allo ws the identification of members of distantly related protein family (motifs) MSA can help us to reveal biological facts about proteins, like analysis of the secondary/tertiary structure 2/22/2018 7
- 8. 2/22/2018 8
- 9. TYPES OF MSA Dynamic programming approach Computes an optimal alignment for a given score function. Because of its high ru nning time , it is not typically used in practice. Progressive method This approach repeatedly aligns two sequences, two alignments, or a sequence with an alignment. Iterative method Works similarly to progressive methods but repeatedly realigns the initial sequence s as well as adding new sequences to the growing MSA. 2/22/2018 9
- 10. PROGRESSIVE ALIGNMENT The most widely used approach Builds up a final MSA by combining pairwise alignments beginning with the most similar pair and progressing to the most distantly r elated Progressive alignment methods require two stages: First stage in which the relationships between the sequences are represented as a tree, called a guide tree ‐Second step in which the MSA is built by adding the sequences sequentially to the growing MSA according to the guide tree 2/22/2018 10
- 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 2/22/2018 11
- 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 2/22/2018 12
- 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 2/22/2018 13
- 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: richa@helix.nih.gov 2/22/2018 14
- 15. STEP 1 2/22/2018 15 Go to https://www.ncbi.nlm.nih.gov/
- 16. STEP 2 The Swiss-Prot protein sequence for Schizosaccharomyces pombe Clr4 is O60016.2. 2/22/2018 16
- 21. Your patience is greatly appreciated…. 2/22/2018 21
- 25. Your patience is greatly appreciated…. 2/22/2018 25
- 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. 2/22/2018 28
- 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. 2/22/2018 31
- 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 2/22/2018 32
- 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/ 2/22/2018 33
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