Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal (or lateral) gene transfer event (xenologs).[1]
Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence. Alignments of multiple sequences are used to indicate which regions of each sequence are homologous.
It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .
Gene prediction is the process of determining where a coding gene might be in a genomic sequence. Functional proteins must begin with a Start codon (where DNA transcription begins), and end with a Stop codon (where transcription ends).
It includes the information related to a bioinformatics tool BLAST (Basic Local Alignment Search Tool), BLAST is in-silico hybridisation to find regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. This presentation too contains the input - output format, Blast process and its types .
Gene prediction is the process of determining where a coding gene might be in a genomic sequence. Functional proteins must begin with a Start codon (where DNA transcription begins), and end with a Stop codon (where transcription ends).
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
Multiple Alignment Sequence using Clustal Omega/ Shumaila RiazShumailaRiaz6
Alignment of three or more biological sequences of Protein, DNA, RNA of similar length
Clustal Omega is tool for analyzing the Multiple sequence alignments of proteins
Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment.
It is also known as substitution matrix.
Scoring matrix of nucleotide is relatively simple.
A positive value or a high score is given for a match & negative value or a low score is given for a mismatch.
Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.
In this presentation, I talk about the various tools for the submission of DNA or RNA sequences into various sequence databases. The sequence submission tools talked about in this presentation are BankIt, Sequin and Webin.
Sequence alig Sequence Alignment Pairwise alignment:-naveed ul mushtaq
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
The Protein Information Resource, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies & contains protein sequences databases
An integrated publicly accessible bioinformatics resource to support genomic/proteomic research and scientific discovery.
Established in 1984, by the National Biomedical Research Foundation (NBRF) Georgetown University Medial Center, Washington D.C., USA.
It is the source of annotated protein databases and analysis tools for the researchers.
Serve as primary resource for the exploration of protein information.
Accessible by text search for entry and list retrieval, and also BLAST search and peptide match.
Multiple Alignment Sequence using Clustal Omega/ Shumaila RiazShumailaRiaz6
Alignment of three or more biological sequences of Protein, DNA, RNA of similar length
Clustal Omega is tool for analyzing the Multiple sequence alignments of proteins
Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment.
It is also known as substitution matrix.
Scoring matrix of nucleotide is relatively simple.
A positive value or a high score is given for a match & negative value or a low score is given for a mismatch.
Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.
In this presentation, I talk about the various tools for the submission of DNA or RNA sequences into various sequence databases. The sequence submission tools talked about in this presentation are BankIt, Sequin and Webin.
Sequence alig Sequence Alignment Pairwise alignment:-naveed ul mushtaq
Sequence Alignment Pairwise alignment:- Global Alignment and Local AlignmentTwo types of alignment Progressive Programs for multiple sequence alignment BLOSUM Point accepted mutation (PAM)PAM VS BLOSUM
The Protein Information Resource, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies & contains protein sequences databases
Bioinformatics is a fast-growing field of study that is providing major solutions to global challenges. It has its applications in the fields of medicine, pharmacology, agriculture, evolution, and environmental management. This document discusses one of the key tools in the field of Bioinformatics - the FastA Homology search algorithm. This document is for academic purposes and does not attempt to exhaust the subject. However, if you would like to discuss the subject in more depth, write to me on my email and we will surely have a discussion. Enjoy the read!
Performance Improvement of BLAST with Use of MSA Techniques to Search Ancesto...journal ijrtem
process in which instead comparing whole query sequence with database sequence it breaks
query sequence into small words and these words are used to align patterns. it uses heuristic method which
make it faster than earlier smith-waterman algorithm. But due small query sequence used for align in case of
very large database with complex queries it may perform poor. To remove this draw back we suggest by using
MSA tools which can filter database in by removing unnecessary sequences from data. This sorted data set then
applies to BLAST which can then indentify relationship among them i.e. HOMOLOGS, ORTHOLOGS,
PARALOGS. The proposed system can be further use to find relation among two persons or used to create
family tree. Ortholog is interesting for a wide range of bioinformatics analyses, including functional annotation,
phylogenetic inference, or genome evolution. This system describes and motivates the algorithm for predicting
orthologous relationships among complete genomes. The algorithm takes a pairwise approach, thus neither
requiring tree reconstruction nor reconciliation
Performance Improvement of BLAST with Use of MSA Techniques to Search Ancesto...IJRTEMJOURNAL
BLAST is most popular sequence alignment tool used to align bioinformatics patterns. It uses
local alignment process in which instead comparing whole query sequence with database sequence it breaks
query sequence into small words and these words are used to align patterns. it uses heuristic method which
make it faster than earlier smith-waterman algorithm. But due small query sequence used for align in case of
very large database with complex queries it may perform poor. To remove this draw back we suggest by using
MSA tools which can filter database in by removing unnecessary sequences from data. This sorted data set then
applies to BLAST which can then indentify relationship among them i.e. HOMOLOGS, ORTHOLOGS,
PARALOGS. The proposed system can be further use to find relation among two persons or used to create
family tree. Ortholog is interesting for a wide range of bioinformatics analyses, including functional annotation,
phylogenetic inference, or genome evolution. This system describes and motivates the algorithm for predicting
orthologous relationships among complete genomes. The algorithm takes a pairwise approach, thus neither
requiring tree reconstruction nor reconciliation
Bioinformatics involves the analysis of biological information using computers and statistical techniques,
In bioinformatics, a 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.
The sequence alignment is made between a known sequence and unknown sequence or between two unknown sequences. The known sequence is called reference sequence. The unknown sequence is called query sequence .
BLAST stands for Basic Local Alignment Search Tool. It addresses a fundamental problem in bioinformatics research. BLAST tool is used to compare a query sequence with a library or database of sequences.
In Bioinformatics, is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences.
BLAST was developed by stochastic model of Samuel Karlin and Stephen Altschul in 1990. They proposed “a method for estimating similarities between the known DNA sequence of one organism with that of another”.
A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query sequence) with a library or database of sequences and identify database sequences that resemble the query sequence above a certain threshold.
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
Honest Reviews of Tim Han LMA Course Program.pptxtimhan337
Personal development courses are widely available today, with each one promising life-changing outcomes. Tim Han’s Life Mastery Achievers (LMA) Course has drawn a lot of interest. In addition to offering my frank assessment of Success Insider’s LMA Course, this piece examines the course’s effects via a variety of Tim Han LMA course reviews and Success Insider comments.
The Roman Empire A Historical Colossus.pdfkaushalkr1407
The Roman Empire, a vast and enduring power, stands as one of history's most remarkable civilizations, leaving an indelible imprint on the world. It emerged from the Roman Republic, transitioning into an imperial powerhouse under the leadership of Augustus Caesar in 27 BCE. This transformation marked the beginning of an era defined by unprecedented territorial expansion, architectural marvels, and profound cultural influence.
The empire's roots lie in the city of Rome, founded, according to legend, by Romulus in 753 BCE. Over centuries, Rome evolved from a small settlement to a formidable republic, characterized by a complex political system with elected officials and checks on power. However, internal strife, class conflicts, and military ambitions paved the way for the end of the Republic. Julius Caesar’s dictatorship and subsequent assassination in 44 BCE created a power vacuum, leading to a civil war. Octavian, later Augustus, emerged victorious, heralding the Roman Empire’s birth.
Under Augustus, the empire experienced the Pax Romana, a 200-year period of relative peace and stability. Augustus reformed the military, established efficient administrative systems, and initiated grand construction projects. The empire's borders expanded, encompassing territories from Britain to Egypt and from Spain to the Euphrates. Roman legions, renowned for their discipline and engineering prowess, secured and maintained these vast territories, building roads, fortifications, and cities that facilitated control and integration.
The Roman Empire’s society was hierarchical, with a rigid class system. At the top were the patricians, wealthy elites who held significant political power. Below them were the plebeians, free citizens with limited political influence, and the vast numbers of slaves who formed the backbone of the economy. The family unit was central, governed by the paterfamilias, the male head who held absolute authority.
Culturally, the Romans were eclectic, absorbing and adapting elements from the civilizations they encountered, particularly the Greeks. Roman art, literature, and philosophy reflected this synthesis, creating a rich cultural tapestry. Latin, the Roman language, became the lingua franca of the Western world, influencing numerous modern languages.
Roman architecture and engineering achievements were monumental. They perfected the arch, vault, and dome, constructing enduring structures like the Colosseum, Pantheon, and aqueducts. These engineering marvels not only showcased Roman ingenuity but also served practical purposes, from public entertainment to water supply.
Instructions for Submissions thorugh G- Classroom.pptxJheel Barad
This presentation provides a briefing on how to upload submissions and documents in Google Classroom. It was prepared as part of an orientation for new Sainik School in-service teacher trainees. As a training officer, my goal is to ensure that you are comfortable and proficient with this essential tool for managing assignments and fostering student engagement.
Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
Sequence homology search and multiple sequence alignment(1)
1. Sequence Homology Search and
Multiple Sequence Alignment
Presented By :
Ankit Tiwari
M.Sc. (MBT)
Final Year
Pt. J.N.M. Medical College Raipur, Chhattisgarh
SESSION : 2018-19
1
2. Contents
Introduction
What is the need of sequence search ???
Homologous sequences
Local and Global Alignment
Pairwise alignment
Heuristic Search Algorithms
Multiple sequence alignment
Why we do multiple alignments ?
Progressive method
References
2
3. Introduction
Sequence similarity searching to identify homologous sequences is one of
the first, and most informative steps in any analysis for newly determined
sequences.
Modern protein sequence databases are very comprehensive, so that
more than 80% of metagenomic sequence samples typically share
significant similarity with proteins in sequence databases.
Widely used similarity searching programs, like BLAST , PSI-BLAST ,
SSEARCH and the HMMER3 programs produce accurate statistical
estimates, ensuring protein sequences that share significant similarity
also have similar structures.
3
4. What is the need of sequence search ?
To find out if a new DNA sequence already is deposited in the databanks.
To find proteins homologous to a putative coding ORF.
To find similar non-coding DNA stretches in the database,
(for example: repeat elements, regulatory sequences).
To compare a short sequence to a large one.
To compare a single sequence to an entire database.
To compare a partial sequence to the whole.
4
5. Homologous sequences
A homologous sequence, in molecular biology, means that the sequence
is similar to another sequence. The similarity is derived from common
ancestry.
Homology among DNA, RNA, or proteins is typically inferred from their
nucleotide or amino acid sequence similarity.
Fig.1 Homologous sequences
Source : https://en.wikipedia.org/wiki/Sequence_homology
5
6. Local and Global Alignment
Local Alignment :
- Stretches of sequences with highest density of matches are aligned.
- Suitable for partially similar different length and conserved region containing
sequences.
Global Alignment :
- Attempts to align the maximum of the entire sequence.
- Suitable for similar and equal length sequences.
6
Fig. 2 local and global alignment
Source : https://www.majordifferences.com/2016/05/difference-between-global-and-local.html#.XAc6W-LhXIU
7. Pair wise Alignment
Pair wise Sequence Alignment is used to identify regions of similarity
that may indicate functional, structural and/or evolutionary
relationships between two biological sequences (protein or nucleic
acid).
It is used to decide if two proteins (or genes) are related structurally or
functionally.
Needleman Wunsch Algorithm Global Alignment
Smith waterman Algorithm Local Alignment
7
8. Heuristic Search Algorithms
A heuristic is a technique designed for solving a problem more quickly
when classic methods are too slow or for finding an approximate solution
when classic methods fail to find any exact solution
Two of the best-known algorithms are FASTA and BLAST.
BLAST- the Basic Local Alignment Search Tool (Altschul et al.,1990), is an
alignment heuristic that determines “local alignments” between a query
and a database. It is based on Smith-Waterman algorithm (local
alignment).
BLAST consists of two components:
1.a search algorithm and
2. a computation of the statistical significance of solutions
8
9. BLAST Program
Program Description
blastp Compares an amino acid query sequence against a
protein sequence database
blastn Compares a nucleotide query sequence against a
nucleotide sequence database
blastx Compares a nucleotide query sequence translated
in all reading frames against a protein sequence
database. You could use this option to find potential
translation products of an unknown nucleotide
sequence.
tblastx Compares the six-frame translations of a
nucleotide query sequence against the six-frame
translations of a nucleotide sequence database
tblastn Compares a protein query sequence against a
nucleotide sequence database dynamically
translated in all reading frames
9
10. Where does the score (S) come
from?
The quality of each pair-wise alignment is
represented as a score and the scores are ranked.
Scoring matrices are used to calculate the score of the
alignment base by base (DNA) or amino acid by amino
acid (protein).
The alignment score will be the sum of the scores for
each position.
10
11. What do the Score and the e-value
really mean?
The quality of the alignment is represented by the Score (S).
The score of an alignment is calculated as the sum of substitution
and gap scores. Substitution scores are given by a look-up table
(PAM, BLOSUM) whereas gap scores are assigned empirically .
The significance of each alignment is computed as an E-value (E).
Expectation value. The number of different alignments with scores
equivalent to or better than S that are expected to occur in a
database search by chance. The lower the E value, the more
significant the score.
11
12. Low E-values suggest that sequences are homologous
Statistical significance depends on both the size of the
alignments and the size of the sequence database.
‣ Important consideration for comparing results across
different searches.
‣ E-value increases as database gets bigger
‣ E-value decreases as alignments get longer
12
13. FASTA
FASTA package was 1st described by Lipman and Pearson in1985.
FASTA is a DNA and protein sequence alignment software.
FASTA is a fast homology search tool.
FAST-P stands for protein , compare the amino acid sequence of
proteins and FAST-N stands for nucleotide alignment, compare
the nucleotide sequence of DNA.
Usually slower than BLAST.
13
14. Multiple Sequence Alignment
Multiple Sequence Alignment (MSA) is generally the alignment of
three or more biological sequence (protein or nucleic acid) of similar
length.
Types of MSA :
i. Dynamic programming
ii. Progressive methods (most commonly used)
iii. Iterative methods
14
15. Why we do multiple alignments?
Multiple nucleotide or amino sequence alignment techniques are
usually performed to fit one of the following scopes :
– In order to characterize protein families, identify shared regions of
homology in a multiple sequence alignment; (this happens generally
when a sequence search revealed homologies to several sequences)
– Determination of the consensus sequence of several aligned
sequences.
– Help prediction of the secondary and tertiary structures of new
sequences.
– Preliminary step in molecular evolution analysis using Phylogenetic
methods for constructing phylogenetic trees.
15
16. Progressive method
This method, also known as the hierarchical or tree method, was
developed by Paulien Hogeweg and Ben Hesper in 1984. It builds up a
final MSA by combining pairwise alignments beginning with the most
similar pair and progressing to the most distantly related pair.
Progressive alignment is a heuristic for multiple sequence alignment
that does not optimize any obvious alignment score. The idea is to do
a succession of pair wise alignments, starting with the most similar
pairs of sequences and proceeding to less similar ones.
16
17. The steps are summarized as follows:
• Compare all sequences pairwise.
• Perform cluster analysis on the pairwise data to generate a hierarchy
for alignment. This may be in the form of a binary tree or a simple
ordering.
• Build the multiple alignment by first aligning the most similar pair of
sequences, then the next most similar pair and so on.
• Once an alignment of two sequences has been made, then this is
fixed.
• Thus for a set of sequences A, B, C, D having aligned A with C and B
with D the alignment of A, B, C, D is obtained by comparing the
alignments of A and C with that of B and D using averaged scores at
each aligned position.
17
18. 18
Fig. 3 Steps of MSA
Source : https://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html
19. References
Feng D.F. and Doolittle R.F. (1987) Progressive sequence alignment
as a prerequisite to correct phylogenetic trees. J. Mol. Evol. ,25,
351–360.
Bedell J and Korf I. BLAST. O’Reilly (P) Ltd;2003 ISBN: 0-596-00299-
8.
Taylor,W.R. (1988) A flexible method to align large numbers of
biological sequences. J. Mol. Evol., 28, 161–169.
19
20. Acknowledgment
I would like to express my sincere gratitude to Dr. Abhigyan Nath sir
for their guidance and help in preparation of this presentation. I
would also like to thanks Dr. G.K. Sahu sir, Dr. Abhigyan Nath sir and
Dr. Khushboo Bhange Ma’am for providing me the opportunity to
present a seminar at this level.
I am also thankful to my classmates for their support in completion
of the assignment.
20