"Sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution."
The analysis of DNA, RNA and protein sequences to infer biological function, evolutionary relationships, and the prediction of gene structure and function.
Alignment algorithms: These are used to compare sequences to identify similarities and differences. Popular examples are Needleman-Wunsch, Smith-Waterman, and ClustalW.
Scoring matrices: These are used to assign scores to aligning sequences, also known as scoring or substitution matrices. Popular examples are BLOSUM and PAM matrices.
Phylogenetic trees: These are used to represent the evolutionary relationships between sequences. They can be constructed using various methods such as maximum likelihood, neighbor joining, and UPGMA.
Hidden Markov Models (HMMs): These are statistical models used for identifying patterns in sequences. They are useful in predicting protein domains, secondary structures, and functional motifs.
Multiple sequence alignment: This involves aligning three or more sequences at a time, and it is useful for studying the conservation of proteins and DNA sequences.
Gene expression analysis: This involves analyzing gene expression profiles across different scenarios, such as under different conditions, time periods or tissues, and correlating them to specific functional pathways.
Proteomics: The study of proteins, including protein expression, modification, and function, and their relationship to disease.
Genomics: The study of large-scale genetic data, including the identification of genes, gene structures, and gene functions.
Transcriptomics: The study of RNA molecules, including identification of alternative splicing events, differential gene expression, and RNA editing.
Epigenomics: The study of epigenetic modifications to DNA, including CpG methylation, histone modification, and non-coding RNA.
Metabolomics: The study of small bio-molecules, including all the intermediate metabolites and end products in a biological system.
Functional genomics: The study of gene and protein functions, including the identification of gene networks, metabolic pathways, and protein-protein interactions.
Systems biology: An interdisciplinary field that combines computational and experimental methods to study biological systems as a whole, including the genetics, physiology, and behavior of organisms.
Pathway analysis: Analysis of biological pathways, including metabolic and signaling pathways, and their relationships to disease and other biological outcomes.
Next-generation sequencing: The use of advanced sequencing technologies to rapidly sequence large amounts of genetic data, facilitating high-throughput sequencing of genomes, transcriptomes, and epigenomes.
Sequence Alignment: It is the process of comparing two or more nucleotide or amino acid sequences to identify regions of similarity or differences.
Phylogenetic Analysis: It is the study of the evolutionary relationships among biological entities, based on comparing and analyzing their genetic evidence.
Motif Analysis: It is the identification of conserved sequence patterns or motifs in DNA, RNA, or protein sequences, which are often associated with functional elements.
Structure Prediction: It is the computation of a reliable 3D-conformation of a protein sequence or RNA molecule from its amino acid or nucleotide sequence.
Genome Annotation: It is the assignment of biological functions to the genes and other functional elements of a genome.
Epitope Prediction: It is the computational approach to predict antigenic properties or epitopes in the amino acid sequence of a protein.
Functional Classification: It is the classification of biological sequences based on their inferred functions or properties.
Comparative Genomics: It is a comparative analysis of the genome sequences from different species or strains to understand evolutionary relationships and functional variations.
Metagenome Analysis: It is the study of the genetic composition of a complex microbial community using high-throughput sequencing and bioinformatics tools.
Protein-Protein Interaction Analysis: It is the identification and analysis of interactions between proteins in a cell or organism using computational or experimental approaches.
"Since the development of methods of high-throughput production of gene and protein sequences, the rate of addition of new sequences to the databases increased very rapidly."
"Comparing these new sequences to those with known functions is a key way of understanding the biology of an organism from which the new sequence comes."
"Nowadays, there are many tools and techniques that provide the sequence comparisons (sequence alignment) and analyze the alignment product to understand its biology."
"Sequence analysis in molecular biology includes a very wide range of relevant topics."
"The comparison of sequences in order to find similarity, often to infer if they are related (homologous)"
"Identification of intrinsic features of the sequence such as active sites, post translational modification sites, gene-structures, reading frames, distributions of introns and exons and regulatory elements."
"Identification of sequence differences and variations such as point mutations and single nucleotide polymorphism (SNP) in order to get the genetic marker."
"Revealing the evolution and genetic diversity of sequences and organisms."
"Identification of molecular structure from sequence alone."
"In chemistry, sequence analysis comprises techniques used to determine the sequence of a polymer formed of several monomers."
"In molecular biology and genetics, the same process is called simply 'sequencing'."
"In marketing, sequence analysis is often used in analytical customer relationship management applications, such as NPTB models (Next Product to Buy)."
"In social sciences and in sociology in particular, sequence methods are increasingly used to study life-course and career trajectories, time use, patterns of organizational and national development, conversation and interaction structure, and the problem of work/family synchrony."
"This body of research is described under sequence analysis in social sciences."
"Sequence analysis can be used to assign function to genes and proteins by the study of the similarities between the compared sequences."
"Methodologies used include sequence alignment, searches against biological databases, and others."
"Such a collection of sequences does not, by itself, increase the scientist's understanding of the biology of organisms."
"Comparing these new sequences to those with known functions is a key way of understanding the biology of an organism from which the new sequence comes."
"The rate of addition of new sequences to the databases increased very rapidly."