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Methods in computational biology
bioinformatics, alignment-free sequence analysis approaches to molecular sequence and structure data provide alternatives over alignment-based approaches
Alignment-free sequence analysis
Alignment-free_sequence_analysis
Process in bioinformatics that identifies equivalent sites within molecular sequences
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
Sequence_alignment
Alignment of more than two molecular sequences
alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences. Alignments
Multiple_sequence_alignment
Identification and study of genomic sequences
that provide the sequence comparisons (sequence alignment) and analyze the alignment product to understand its biology.Sequence analysis in molecular biology
Sequence_analysis
specialized on: Sequence analysis software List of sequence alignment software List of alignment visualization software Alignment-free sequence analysis De novo
Lists of bioinformatics software
Lists_of_bioinformatics_software
of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See
List of sequence alignment software
List_of_sequence_alignment_software
related genomes is similar. Gene signature mutational signatures Alignment-free sequence analysis Bioinformatics Computational genomics K-mer Phylogenomics Kariin
Genomic_signature
File format for gene sequences
Sequence Alignment Map (SAM) is a text-based format originally for storing biological sequences aligned to a reference sequence developed by Heng Li and
SAM_(file_format)
This page is a subsection of the list of sequence alignment software. Multiple alignment visualization tools typically serve four purposes: Aid general
List of alignment visualization software
List_of_alignment_visualization_software
Succession of nucleotides in a nucleic acid
manipulations of the information profiles enable the analysis of the sequences using alignment-free techniques, such as for example in motif and rearrangements
Nucleic_acid_sequence
Software package for sequence analysis
HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or
HMMER
Aligning molecular sequences using sequence and structural information
acid sequences converge on a common tertiary structure. Structural alignments can compare two sequences or multiple sequences. Because these alignments rely
Structural_alignment
Substrings of length k contained in a biological sequence
important method in alignment-free sequence analysis. It can also be used as a first stage analysis before an alignment. In sequence assembly, k-mers are
K-mer
M, Barton GJ (May 2009). "Jalview Version 2--a multiple sequence alignment editor and analysis workbench". Bioinformatics. 25 (9): 1189–1191. doi:10
List of RNA structure prediction software
List_of_RNA_structure_prediction_software
Grammar model in linguistics
a valid derivation using an automaton. Parse Tree: The alignment of the grammar to a sequence. An example of a parser for PCFG grammars is the pushdown
Probabilistic context-free grammar
Probabilistic_context-free_grammar
Bioinformatics search algorithm
local alignment search tool) is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins
BLAST_(biotechnology)
Algorithm for determining similar regions between two molecular sequences
performs local sequence alignment; that is, for determining similar regions between two strings of nucleic acid sequences or protein sequences. Instead of
Smith–Waterman_algorithm
Analysis of sets of categorical sequences
sequence analysis (SA) is concerned with the analysis of sets of categorical sequences that typically describe longitudinal data. Analyzed sequences are
Sequence analysis in social sciences
Sequence_analysis_in_social_sciences
(Context-Specific BLAST) is a tool that searches a protein sequence that extends BLAST (Basic Local Alignment Search Tool), using context-specific mutation probabilities
CS-BLAST
Lists of software used in various branches of engineering
robotics software List of scientific simulation software List of sequence alignment software List of software for nanostructures modeling List of software
Lists_of_engineering_software
Branch of bioinformatics
areas of the life sciences. This includes visualization of sequences, genomes, alignments, phylogenies, macromolecular structures, systems biology, microscopy
Biological_data_visualization
Molecular modelling software
visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results
UCSF_Chimera
Computer software for bioinformatics
to analyze various biological genetics data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. UGENE
UGENE
Square matrix containing the distances between elements in a set
then obtain the local alignment. Multiple sequence alignment is an extension of pairwise alignment to align several sequences at a time. Different MSA
Distance_matrix
Pan-genome Graph Construction Methodology
inclusive representation allows for unbiased analysis of genomic data, significantly improving sequencing read alignment, variant detection, and genotyping accuracy
Pan-genome_graph_construction
Conformance of AI to intended objectives
In the field of artificial intelligence (AI), alignment aims to steer AI systems toward a person's or group's intended goals, preferences, or ethical
AI_alignment
Analysis Package) is a suite of bioinformatics software tools from the BGI Bioinformatics department enabling the assembly, alignment, and analysis of
Short Oligonucleotide Analysis Package
Short_Oligonucleotide_Analysis_Package
Bioinformatics computer program
Clustal is a computer program used for multiple sequence alignment in bioinformatics. It is one of the most widely cited bioinformatics software with two
Clustal
RNA-Seq analysis involves alignment of the sequenced reads to a reference genome (if available) or to a transcriptome database. See also List of sequence alignment
List of RNA-Seq bioinformatics tools
List_of_RNA-Seq_bioinformatics_tools
Bioinformatics software suite
Alignments), a tool for Sequence Alignment, is the latest incarnation of software originally developed at The University of Leeds to aid the analysis
UTOPIA_(bioinformatics_tools)
Study of RNA transcripts
can be used as a reference for subsequent sequence alignment methods and quantitative gene expression analysis. Legend: RAM – random access memory; MPI
Transcriptomics_technologies
Study of viral material
databases and high viral sequence divergence. On the other hand, alignment-free methods– using features such as k-mer composition analysis, codon usage, and
Virome_analysis
File format for DNA or protein sequences
the actual sequence is represented. Sequences may be protein sequences or nucleic acid sequences, and they can contain gaps or alignment characters (see
FASTA_format
Protein sequences. A free demo is available from the software developers website. DNADynamo is a general purpose DNA and Protein sequence analysis package
DNADynamo
Collection of open-source Python software tools for computational biology
into their software. Biopython contains a standard sequence class, sequence alignment, and motif analysis tools. It also has clustering algorithms, a module
Biopython
Software project for the analysis of genomic data
Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments
Bioconductor
DNA section marked with start and stop codon of different length
deduced amino acid sequence can be saved in various formats and searched against the sequence database using the basic local alignment search tool (BLAST)
Open_reading_frame
Free software package for phylogenetic analysis of rRNA
Project is a free software package for the phylogenetic analysis of rRNA and other biological sequences including DNA and protein sequence. It provides
ARB_Project
Suite of free genome analysis software by Nvidia
acquired by Nvidia in 2020. Nvidia Parabricks is a suite of free software for genome analysis developed by Nvidia, designed to deliver high throughput by
Nvidia_Parabricks
File format for biological sequence alignments
a multiple sequence alignment format used by Pfam, Rfam and Dfam, to disseminate protein, RNA and DNA sequence alignments. The alignment editors Ralee
Stockholm_format
Data mining technique
classified as global alignments, semi-global alignments and local alignment. See sequence alignment. Some problems in sequence mining lend themselves
Sequential_pattern_mining
Lab technique in cellular biology
Wysoker A, Fennell T, Ruan J, Homer N, et al. (August 2009). "The Sequence Alignment/Map format and SAMtools". Bioinformatics. 25 (16): 2078–9. doi:10
RNA-Seq
Method of genome sequencing
section. DNA sequencing Sequence analysis Sequence assembly Coverage (genetics) Taxonomy (biology) Alignment-free sequence analysis Computational phylogenetics
Genome_skimming
Field of biological research
mining Molecular evolution Comparative anatomy Homology Sequence mining Alignment-free sequence analysis Darling AE, Miklós I, Ragan MA (July 2008). "Dynamics
Comparative_genomics
Computational analysis of large, complex sets of biological data
into three categories: SSS (Sequence Search Services), MSA (Multiple Sequence Alignment), and BSA (Biological Sequence Analysis). The availability of these
Bioinformatics
Statistical Markov model
recognition Alignment of bio-sequences Time series analysis Activity recognition Protein folding Sequence classification Metamorphic virus detection Sequence motif
Hidden_Markov_model
Open source software analysis package
applications for sequence alignment, rapid database searching with sequence patterns, protein motif identification (including domain analysis), and much more
EMBOSS
Tertiary structure prediction tool for protein sequence
discerned through sequence alignment. Currently the most powerful and accurate methods for detecting and aligning remotely related sequences rely on profiles
Phyre
Description of the structure and function of a genome
"Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification". Microbial Genomics. 7 (11). doi:10.1099/mgen.0
DNA_annotation
Topics referred to by the same term
Acoustic Medicine, a medical treatment for arthritis SAMtools (for Sequence Alignment Map), a data storage format for DNA sequencing Self-assembled monolayer
Sam
Topics referred to by the same term
cereal, rice, and milk diet CRAM (file format), a compressed genome sequence alignment file Cramming (education), a slang term for last-minute study Cramming
Cram
Astrophotography software application
large number of formats (images or videos) to FITS. The calibration, alignment and stacking of astronomical images is done by navigating through the
Siril_(software)
Pairwise sequence alignment algorithm
BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC)
BLAT_(bioinformatics)
Bioengineering process
sequence alignments for the target sequence. This alignment is then subjected to manual refinement that involves removal of highly gapped sequences,
Protein_engineering
Type of biological prediction
situation improves somewhat when the amino acid variation in multiple sequence alignments is taken into account. Parts of the protein may have fixed three-dimensional
Protein_structure_prediction
Model of changes in a sequence over evolutionary time
to calculate the likelihood of phylogenetic trees using multiple sequence alignment data. Thus, substitution models are central to maximum likelihood
Substitution_model
Compilation of software used to produce phylogenetic trees
2014). "AliGROOVE--visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support". BMC
List of phylogenetics software
List_of_phylogenetics_software
Methylation process
samples. Various software for alignment and analysis is available, such as Maq, BS Seeker, Bismark or BSMAP. Alignment to a reference genome allows the
Reduced representation bisulfite sequencing
Reduced_representation_bisulfite_sequencing
computational and statistical analysis to decipher biology from genome sequences and related data, including both DNA and RNA sequence as well as other "post-genomic"
Computational_genomics
Computational prediction of nucleic acid structure
Folding of alignment Alignment of singular predicted structures, in some cases jointly with sequence alignment Simultaneous alignment of sequence and ensembles
Nucleic acid structure prediction
Nucleic_acid_structure_prediction
structure comparison, pairwise and multiple sequence alignments, working with DNA and protein sequences, analysis of amino acid properties, detecting protein
BioJava
Topics referred to by the same term
a period of African prehistory Multiple sequence alignment, an alignment of three or more biological sequences Multiple system atrophy, a degenerative
MSA
Average solution cost is the same with any method
"Coevolutionary free lunches," IEEE Transactions on Evolutionary Computation, 9(6): 721–735 A search algorithm also outputs the sequence of candidate solutions
No free lunch in search and optimization
No_free_lunch_in_search_and_optimization
Database branch of the US National Library of Medicine
directed by David Lipman, one of the original authors of the BLAST sequence alignment program and a widely respected figure in bioinformatics. The US National
National Center for Biotechnology Information
National_Center_for_Biotechnology_Information
Engineering discipline focused on the design and operation of chemical plants
operation, including safety and hazard assessments, process design and analysis, modeling, control engineering, chemical reaction engineering, nuclear
Chemical_engineering
Approach to the study of social interaction
ISBN 9780521552257. Schegloff, Emanuel A. (2007). Sequence organization in interaction: a primer in conversation analysis. Cambridge, UK: Cambridge University Press
Conversation_analysis
Branch of engineering which deals with the optimization of complex processes or systems
social sciences together with the principles and methods of engineering analysis and design, to specify, predict, and evaluate the results to be obtained
Industrial_engineering
Group of evolutionarily-related proteins
between sequences use sequence alignment methods. Proteins that do not share a common ancestor are unlikely to show statistically significant sequence similarity
Protein_family
Repeating sequences of 2–13 base pairs of DNA
human microsatellites revealed by human-chimpanzee-orangutan genomic sequence alignments". Journal of Molecular Evolution. 71 (3): 192–201. Bibcode:2010JMolE
Microsatellite
Adjacent repeated pattern of nucleotides within DNA
Pavel A. (September 2023). "UniAligner: a parameter-free framework for fast sequence alignment". Nature Methods. 20 (9): 1346–1354. bioRxiv 10.1101/2022
Tandem_repeat
Combination of electronics and mechanics
structure prediction Robotics simulation Scientific simulation Sequence alignment Structural alignment Structural engineering System dynamics Wind energy Engineering
Mechatronics
tertiary structure of an amino acid sequence is predicted based on a sequence alignment to a template, or a second sequence whose structure is known. Because
Loop_modeling
Software for understanding biological data
a comparison was done by means of multiple sequence alignment. Machine learning methods for the analysis of neuroimaging data are used to help diagnose
Machine learning in bioinformatics
Machine_learning_in_bioinformatics
Open source bioinformatics software developed by Ian Holmes
multiple RNA sequence alignment and RNA structure prediction based on probabilistic models of RNA structure known as Pair stochastic context-free grammars
Stemloc
Use of software for engineering design and analysis
in tasks related to engineering analysis. Computer-aided engineering (CAE) includes finite element method or analysis (FEA), computational fluid dynamics
Computer-aided_engineering
German researcher and professor of bioinformatics
thesis, titled "A Polyhedral Approach to Sequence Alignment Problems", focused on solving NP-hard sequence alignment problems for Proteins and RNA using methods
Knut_Reinert
classifiers exploit the previously known sequences by performing alignments against databases, and try to separate sequence based in organism-specific characteristics
Binning_(metagenomics)
for molecular mechanics modeling Earth BioGenome Project List of sequence alignment software List of open-source healthcare software List of biomedical
List of open-source bioinformatics software
List_of_open-source_bioinformatics_software
Graphical representation of music
de facto standard for tasks such as music alignment and synchronization as well as audio structure analysis. Finally, chroma features have turned out
Chroma_feature
in the protein. The method relies on an input sequence alignment between the target amino acid sequence to be modeled and a template protein which structure
MODELLER
which are relatively simple. Programs for the analysis of DNA sequence alignments, protein sequence alignments, or discrete characters (e.g., morphological
PHYLIP
Lab procedure detecting 5-methylcytosines in DNA
analyses can be performed on the altered sequence to retrieve this information. The objective of this analysis is therefore reduced to differentiating
Bisulfite_sequencing
Sub-discipline of electrical engineering
some of the most popular. Electronic signal processing deals with the analysis and manipulation of signals. Signals can be either analog, in which case
Electronics_engineering
Academic discipline and occupational field
thickness used in pavement designing the geometry (vertical and horizontal alignment) of the roadway (or track). Before any planning occurs an engineer must
Transportation_engineering
Genome browser hosted by the University of California, Santa Cruz
studies. Tools like BLAT (BLAST-like alignment tool) and LiftOver were introduced to enhance sequence alignment and coordinate conversion between different
UCSC_Genome_Browser
Database of protein families
of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The latest version of Pfam
Pfam
Bioinformatics subfield
evolutionary relationship among a set of proteins even with low sequence similarity. Structural alignment implies superimposing a 3D structure over a second one
Structural_bioinformatics
structure prediction Robotics simulation Scientific simulation Sequence alignment Structural alignment Structural engineering System dynamics Wind energy Engineering
List of civil engineering software
List_of_civil_engineering_software
Overview of and topical guide to algorithms
algorithm-performance analysis Amortized analysis — analysis of average cost over a sequence of operations Competitive analysis (online algorithm) — analysis of online
Outline_of_algorithms
Needleman–Wunsch algorithm: find global alignment between two sequences Smith–Waterman algorithm: find local sequence alignment Exchange sorts Bubble sort: for
List_of_algorithms
Study of making products from raw materials
Processes where phase change and phase equilibria are relevant require analysis using the principles and laws of thermodynamics to quantify changes in
Process_engineering
used for computational fluid dynamics, finite element method structural analysis, flight dynamics, propulsion modeling, and other related engineering applications
List of aerospace engineering software
List_of_aerospace_engineering_software
Random process independent of past history
Ferreira, P (May 18, 2015). "An alignment-free method to find and visualise rearrangements between pairs of DNA sequences". Scientific Reports. 5 (10203)
Markov_chain
Protein-coding gene in the species Homo sapiens
domain. However, a NCBI BLAST alignment of just the amino acids from 297 to 400 does illustrate that the latter sequence is indeed a fourth immunoglobulin
Alpha-1-B_glycoprotein
Suite of services for protein homology modeling
modelling steps: automated mode, alignment mode, and project mode. A fully automated mode is used when a sufficiently high sequence identity between target and
Swiss-model
Method of analyzing transmission electron microscopy imagery
"Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences". Nature Communications. 15 (1) 8808. Bibcode:2024NatCo
Single_particle_analysis
recognition system. HPCP are an enhanced pitch distribution feature that are sequences of feature vectors that, to a certain extent, describe tonality, measuring
Harmonic_pitch_class_profiles
Engineering approach to software development
activities that were formerly called computer programming and systems analysis As the broad term for all aspects of the practice of computer programming
Software_engineering
located in the chromosome (C). Further homology and structure conservation analysis have identified full-length Smr9C homologs in several nitrogen-fixing symbiotic
Αr9_RNA
Branch of phylogeny that analyzes genetic, hereditary molecular differences
most common approach is the comparison of homologous sequences for genes using sequence alignment techniques to identify similarity. Another application
Molecular_phylogenetics
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