- ab initio
- gene finding
- tertiary protein structure prediction
- (AC)n repeat motif in birds
- ACCAUGG sequence
- accessible surface area (ACC; solvent accessibility)
- accession number
- GenBank
- in BLASTn
- in BLASTx
- in tBLASTn
- in tBLASTx
- in restriction enzyme site detection (using NEBCUTTER)
- active sites (of receptor)
- adapter
- additivity of distances
- algorithm
- alignments (sequence)
- allosteric protein
- alpha helices
- amino acids (AAs)
- analysis using Sequence Manipulation Suite
- color scheme for AA residues
- IUPAC codes
- number of identical AA residues
- sequence (primary structure of protein)
- alignment search tools (in BLAST)
- in online secondary structure prediction
- in prokaryotic genome annotation
- retrieval
- amplicon
- size
- optimal
- secondary structure checking
- SYBR green chemistry of qPCR
- amplification of DNA see DNA
- analogs
- annealing in PCR primer design
- oligo concentration
- SYBR green chemistry of qPCR
- temperature
- annotation
- Antisense Design, IDT
- Arabidopsis thaliana miRNA targets
- archaea gene finding
- arithmetic mean
- definition
- unweighted‐pair group method with (UPGMA)
- weighted‐pair group method with (WPGMA)
- Assembly (NCBI)
- ATG codon
- AUG codon
- avians (birds), (AC)n repeat motif
- bacterial gene finding
- bacteriophages (phages), gene finding
- BAM/BAM files (binary alignment/map)
- differential gene expression
- RNA‐Seq
- barcode
- bases
- beta‐lactoglobulin
- beta sheets (β‐sheets)
- binary alignment/map see BAM
- binary tree
- binding site
- pocket multiplicity
- transcription factor
- Bioconductor
- bioinformatics, definition
- Bioinformatics and Functional Genomics
- biological replicates in microarray data analysis of gene expression
- Biology Project
- Biology Related Internet Sites
- Bioproject (NCBI)
- Biosample
- biostatistics
- Biosystems (NCBI)
- birds, (AC)n repeat motif
- bit score (S’)
- BLAST
- BLASTn
- BLASTp
- BLASTx
- translated (tBLASTx)
- see also tBLASTx
- Bonferroni corrections
- books, online/internet
- Bookshelf
- bootstrapping
- maximum parsimony method
- MEGA7 method
- bovines (cattle incl. Bos taurus)
- differential gene expression
- Drosha
- functional annotation
- microarray analysis
- protein structure
- Bowtie
- branches
- length
- in Fitch–Margoliash algorithm
- horizontal
- of internal node
- in Jukes–Cantor one‐parameter substitution model
- in Kimura’s two parameter substitution model
- in MEGA7
- in minimum evolution method
- in neighbor‐joining method
- in unweighted‐pair group method with arithmetic mean
- bridge amplification
- Burrows–Wheeler Algorithm (BWA)
- with GATK
- in RNA‐seq alignment
- with Stacks
- Burrows–Wheeler transform
- C++ Toolkit (NCBI)
- CAGGTAGGTG (Seq2)
- in global alignment
- in local alignment
- cancer
- cations in PCR primary design
- quality checking of designed primer
- cattle see bovines
- CCDS (Consensus CDS)
- CDD (Conserved Domains Database)
- CDM tool
- character‐based methods of phylogenetic tree construction
- ChIP fragments
- chromatin immunoprecipitation (ChIP) fragments
- chronogram
- CINEMA 2.1 (Color INteractive Editor for Multiple Alignments)
- circular sequence (NebCutter)
- circular tree
- clade
- cladistics
- cladogram
- CLASS table
- ClinVar (NCBI)
- Clone DB
- ClueGO
- CLUSTAL (clustal)
- /.ALN format
- Omega
- W
- W2
- X
- clustering/cluster analysis
- c‐MYC
- Coding (ENA database)
- codon
- Color INteractive Editor for Multiple Alignments (CINEMA 2.1)
- color scheme for amino acid residues
- Combine FASTA
- comparative protein modeling
- Complete PCR Solution
- Comprehensive Perl Archive Network (CPAN)
- Comprehensive R Archive Network (CRAN)
- Computational Resources from NCBI’s Structure Group
- Consensus CDS (CCDS)
- Consensus Data Mining (CDM)
- Conserved Domains Database (CDD)
- coverage in Ref‐Seq
- CPAN (Comprehensive Perl Archive Network)
- CpG islands
- CRAN (Comprehensive R Archive Network)
- cross‐dimers (hetero‐dimers)
- Ct values
- CTAGTAG (Seq1)
- in global alignment
- in local alignment
- Cuffdiff
- Cufflinks
- differentially gene expression
- RNA‐Seq
- Cuffmerge
- Cytoscape
- database(s)
- Database for Annotation, Visualization and Integrated Discovery (DAVID)
- Database of Expressed Sequence Tags
- Database of Genomic Structural Variation (dbVar)
- Database of Genotypes and Phenotypes (dbGaP)
- Database of Major Histocompatibility Complex (dbMHC)
- Database of Short Genetic Variations (dbSNP)
- DAVID (Database for Annotation, Visualization and Integrated Discovery)
- DbClustal
- dbEST (database of expressed sequence tags)
- dbGaP (Database of Genotypes and Phenotypes)
- dbGSS (Genome Survey Sequence database)
- dbMHC (Database of Major Histocompatibility Complex)
- dbSNP (Database of Short Genetic Variations)
- dbVar (Database of Genomic Structural Variation)
- DDBJ (DNA Databank of Japan)
- de novo methods
- comparative protein modeling
- SNP mining
- deep sequencing
- deletion see insertion and deletion
- delta BLAST
- delta Ct values
- dendrogram
- deoxynucleotide triphosphate (dNPT) in PCR primer design
- quality checking of designed primer
- DESeq2
- differentially expressed genes
- common, functional annotation
- identification
- dihedral angle
- Discontiguous MegaBLAST
- distance (values)
- global distance test
- in neighbor‐joining method
- pairwise
- in unweighted‐pair group method with arithmetic mean
- distance matrix
- in minimum evolution method
- in neighbor‐joining method
- in unweighted‐pair group method with arithmetic mean
- distance scale
- divalent cations in PCR primary design
- divergence
- DNA
- filter, in sequence analysis
- Mutate DNA
- patented
- sequence
- transcription factor binding sites
- DNA Databank of Japan (DDBJ)
- DNA Molecular Weight
- DNA Pattern Find
- DNA Range Extractor, in sequence analysis
- DNA Stats
- docking (molecular)
- domain
- partition in tertiary protein structure prediction
- domain enhanced look‐up time accelerated (DELTA) BLAST
- dot plot analysis
- Dotlet
- Dotplot(+)
- Dotter
- Drosha taurine cattle
- dynamic programming
- miRNA target prediction
- Needleman–Wunsch algorithm
- RNA‐Seq data analysis
- Smith–Waterman algorithm
- E‐value (expectation value; threshold value)
- EBI (European Bioinformatics Institute)
- EBSeq
- EDAM (EMBL)
- edge length
- edgeR
- Electronic Protocol Book
- EMBL
- databases
- Feature Extractor
- tools
- Trans Extractor
- EMBOSS (European Molecular Biology Open Software Suite)
- ENA (European Nucleotide Archive)
- energy functions
- Ensembl
- Entrez Query
- BLASTn
- BLASTp
- BLASTx
- Primer‐BLAST
- tBLASTn
- tBLASTx
- Epigenomics
- eukaryotes
- gene annotation/finding
- genome database
- European Bioinformatics Institute (EBI)
- European Molecular Biology Open Software Suite see EMBOSS
- European Nucleotide Archive (ENA)
- European Patent Office Proteins
- evolution
- change through time (phenogram)
- geological events
- minimum (ME method)
- molecular
- molecular phylogeny and
- rate
- in converting unrooted tree to rooted tree
- in Fitch–Margoliash algorithm
- in MEGA7
- in minimum evolution method
- in neighbor‐joining method
- in unweighted‐pair group method with arithmetic mean (UPGMA)
- relatedness/relationships among taxa in
- cladistics revealing
- dendrogram revealing
- Exclude Models(XM/XP)
- BLASTp
- BLASTx
- tBLASTn
- tBLASTx
- exons in genome annotation
- eukaryotes
- prokaryotes
- in RNA‐seq alignment
- ExPASy (Expert Protein Analysis System)
- expectation value see E‐value
- Expert Protein Analysis System (ExPASy)
- expressed sequence tags (EST)
- external nodes
- F81 model
- FACTORS table
- FASTA (fast all)
- in BLASTn
- in BLASTp
- Combine
- in differential gene expression
- in microRNA expression
- in online/internet alignment tools
- in PCR primer design
- in phylogenetic tree construction
- in restriction enzyme site detection (using NEBCUTTER)
- in secondary protein structure prediction
- in Sequence Manipulation Suite
- in tertiary protein structure prediction
- in tLASTn
- in tLASTx
- in translation initiation site prediction
- FASTA/Pearson format
- FASTM
- FastPCR
- Fastq file
- FASTX Tool Kit
- Feature Extractor
- Felenstein model (1981)
- File Transfer Protocol (FTP)
- filter DNA in sequence analysis
- filter protein in sequence analysis
- Fitch (F)
- Fitch–Margoliash algorithm
- fluorescence chemistry
- microarray data analysis
- for real‐time PCR
- FMTSeq
- fold change (in gene expression)
- fold recognition (=threading method)
- FPKM (fragment per kilobase of exon per million mappable reads)
- free energy
- FTP (File Transfer Protocol)
- functional analysis of proteins
- functional annotation
- common differentially expressed genes
- functional information using gene networks and pathways
- gamma parameter
- gap‐penalty
- Needleman–Wunsch algorithm
- Smith–Waterman algorithm
- GC clamp (PCR primers)
- SYBR green chemistry of qPCR
- GC content (PCR primers)
- genome annotation in eukaryotes
- SYBR green chemistry of qPCR
- GCCGCCACCAUGG sequence
- GCG format
- GCTA (Genome‐wide Complex Trait Analysis)
- GenBank (NCBI)
- accession number see accession number
- Feature Extractor
- sequence format conversion
- Taxonomy Database
- Trans Extractor
- Gene (NCBI database)
- gene(s)
- Gene Expression Omnibus (GEO)
- gene transfer format (GTF) files
- GeneMark
- GeneReviews
- Genes and Disease (NCBI database)
- GeneTests
- genetic code
- in BLASTx
- in restriction enzyme site detection
- restriction enzyme site detection
- in Sequence Manipulation Suite
- in tBLASTx
- see also codon
- Genetic Testing Registry (GTR)
- Genetics Computer Group (GCG) format
- Genetics Education Centre
- genome
- Genome Analysis Toolkit (GATK)
- Genome (NCBI database)
- Genome Reference Consortium
- Genome Survey Sequence (dbGSS)
- Genome Survey Sequences (GSS)
- Genome‐wide Complex Trait Analysis (GCTA)
- Genome2Seq
- Genomes Gene (Ensembl)
- Genomes Transcript (Ensembl)
- Genomic Mapping and Alignment Program (GMAP)
- Genomic Short‐read Nucleotide Alignment Program (GSNAP)
- genomics
- Genotypes and Phenotypes, database of (dbGaP)
- GEO (Gene Expression Omnibus)
- geological clock
- Geospatial (ENA database)
- Gibbs free energy see free energy
- global alignment
- Needleman–Wunsch algorithm
- Smith–Waterman algorithm
- global distance test
- global normalization of microarray data
- Glossary (NCBI)
- GMAP
- GOLD (Genomes online database)
- g:Profiler
- GRC (Genome Reference Consortium)
- GSNAP
- GTF (gene transfer format) files
- GTR (Genetic Testing Registry)
- guide‐tree
- max guide tree iterations
- mBed‐like Clustering
- gunzipping of files
- hairpin (stem‐loop)
- in dot plot analysis
- PCR primers
- Handbook (NCBI)
- health (human) and ClinVar
- Help Manual (NCBI)
- hetero‐dimers (cross‐dimers)
- heuristic program
- HGNC (HUGO Gene Nomenclature Committee)
- hidden Markov model (HMM)
- High‐Mobility Group AT‐hook 2 (HMGA2)
- high‐scoring segment pair (HSP)
- high‐throughput sequencing and data see next generation/high‐throughput sequencing and data
- HIV‐1, Human Protein Interaction Database
- HLA/MHC databases
- HMGA2
- homing endonucleases
- homodimer (self‐dimers)
- HomoloGene
- homology (and homologous sequences)
- horizontal branch length
- HTTP (Hyper Text Transfer Protocol)
- HUGO Gene Nomenclature Committee
- human
- evolution
- health, ClinVar (NCBI) and its relationship to
- miRNA target prediction
- Human Genome Browser
- human immunodeficiency virus (HIV‐1), Human Protein Interaction Database
- Human Microbiome Project
- hybridizations, repeat, in microarray data analysis of gene expression
- Hyper Text Transfer Protocol (HTTP)
- IDT (Integrated DNA Technologies)
- Antisense Design
- OligoAnalyzer
- UnaFold
- Illumina
- image processing in microarray data analysis
- IMGT/HLA (International ImMunoGeneTics) databases
- immunoglobulin database
- in silico sequence analysis
- InDel and Indels see insertion and deletion
- Influenza Virus (NCBI database)
- insertion and deletion(s) (InDel and Indels)
- Integrated DNA Technologies see IDT
- internal nodes
- branch length of
- distance with (Z)
- distance of other OTUs from
- in MEGA7
- in neighbor‐joining method
- in unweighted‐pair group method with arithmetic mean (UPGMA)
- International ImMunoGeneTics (IGMT) databases
- International Nucleotide Sequence Database Collaboration
- International Union of Pure and Applied Chemistry (IUPAC) codes
- internet see online
- InterPro
- introns
- BLASTn
- in genome annotation
- IP (Internet Protocol) address
- IPD‐KIR
- IPD‐MHC
- isoelectric point of protein
- iterations
- of EBSeq
- max guide tree iterations
- max HMM iterations
- in neighbor‐joining method
- number of combined iterations
- IUPAC see International Union of Pure and Applied Chemistry
- JALVIEW (Java ALignmentVIEWer)
- Japanese Patent Office Proteins (JPO proteins)
- Java ALignmentVIEWer (JALVIEW)
- JC69 (Jukes–Cantor) model
- Jones–Taylor–Thornton (JTT) model
- Journals in NCBI Databases
- JPO Proteins (Japanese Patent Office Proteins)
- Jukes–Cantor (JK69) model
- junction reads
- K80 model
- KEGG (Kyoto Encyclopedia of Genes and Genomes)
- killer cell immunoglobulin‐like receptors (KIR) IPD‐KIR database (IPD‐KIT)
- Kimura’s two parameter substitution model
- KIPO (Korean Intellectual Property Office) Proteins
- Kozak consensus sequence
- Kyoto Encyclopedia of Genes and Genomes (KEGG)
- LALIGN
- leaf (leaves)
- least‐distant pair
- libraries
- binding site searches
- differentially expressed genes
- ligand
- binding site see binding site
- docking
- selection and preparation
- “Limits” option
- nucleotide sequence retrieval from NCBI nucleotide database
- tBLASTx
- linear sequence (NebCutter)
- Livak method
- livestock research, microarray analysis
- local alignment
- nucleotides (incl. BLASTn)
- protein (amino acid) sequences (in BLAST)
- Smith–Waterman algorithm
- local sequence file in NebCutter
- long branch attraction
- long read aligners
- loop design in microarray data analysis of gene expression
- MACAW (Multiple Alignment Construction and Analysis Workbench)
- MAFFT (Multiple Alignment using Fast Fourier Transform)
- magnesium ions (Mg+) concentration in PCR primer quality checking
- major histocompatibility complex databases
- mammary glands, bovine
- Mapper
- Markov model, hidden see hidden Markov model
- matrix construction, initiation
- in Needleman–Wunsch algorithm
- in Smith–Waterman algorithm
- max guide tree iterations
- max HMM iterations
- Max Score (BLASTn)
- Maximum Identity (BLASTn)
- maximum likelihood (ML) tree
- maximum parsimony (MP) method
- mBed‐like Clustering Guide‐tree
- Medical Subject Headings database (MeSH)
- MEDLINE
- MEGA7
- MegaBLAST
- MEGAN 4 (MEtaGenome ANalyzer)
- melting temperature (Tm) of PCR primers
- Mendelian Inheritance (Online)
- MendelWeb
- MeSH (Medical Subject Headings db)
- messenger RNA see RNA
- metagenomes
- databases
- gene prediction
- Metagenomic Proteins in BLASTp
- metatranscriptomes, gene prediction
- MG‐RAST
- MHC (major histocompatibility complex; HLA) databases
- microarray
- next‐generation sequencing addressing limitations
- probe
- microbiome (in humans)
- microRNA see RNA
- microsatellites, in silico mining
- minimum evolution (ME) method
- miRBase
- MiRDeep and MiRDeep2
- MISA (microsatellite identification tool)
- mismatch
- melting temperature mismatch of PCR primers
- mismatch limit in dot plot analysis
- mismatch penalty in Smith–Waterman algorithm
- mispriming
- SYBR green chemistry of qPCR
- Molecular Biology Web Book
- molecular clock
- molecular evolution
- Molecular Evolution and Genetic Analysis‐7 (MEGA7)
- Molecular Modeling Database (MMDB)
- molecular phylogeny see phylogeny
- molecular weight (program determining)
- MOLprobity
- monophyletic group
- monovalalent cations in PCR primary design
- quality checking of designed primer
- morphological phylogeny
- motif
- Multiple Alignment Construction and Analysis Workbench (MACAW)
- Multiple Alignment using Fast Fourier Transform (MAFFT)
- multiple sequence alignments (MSA)
- databases
- in phylogenetic tree construction
- Multiple Sequence Comparison by Log‐Expectation (MUSCLE)
- MUSCLE (Multiple Sequence Comparison by Log‐Expectation)
- Mutate DNA
- Mutate for Digest
- MUTATE Protein
- mutations
- Mview
- National Center for Biotechnology Information (NCBI)
- BLAST see BLAST
- databases
- nucleotide sequence retrieval
- National Institutes of Health (NIH) online resources
- NCNI see National Center for Biotechnology Information
- NDB (Nucleic Acid Database)
- NEBCutter
- Needleman–Wunsch algorithm
- neighbor‐joining (NJ) method
- NetStart
- next generation/high‐throughput sequencing and data (NGS)
- microRNA expression
- Ref‐Seq data analysis
- SNPs
- NIH online resources
- nodes
- non‐coding RNA (ENA database)
- non‐redundant patent proteins level 1 and 2
- normalization (of data)
- differential gene expression
- microarray
- RNA‐seq
- Notes on Population Genetics
- Nucleic Acid Database (NDB)
- nucleotide(s)
- Nucleotide Database (NCBI)
- nucleotide sequences
- Basic Local Alignment Search Tool for (BLASTn)
- in gene finding
- in genome annotation
- in eukaryotes
- in prokaryotes
- in PCR primer design
- in phylogenetic tree construction
- in MEGA7 method
- in minimal evolution method
- restriction enzyme digestion see restriction enzymes
- retrieval from NCBI nucleotide database
- Sequence Manipulation Suite (SMS) in analysis of
- in single nucleotide polymorphism mining
- in transcription factor binding site prediction
- translated Basic Local Alignment Search Tool for (yBLASTn)
- in translation initiation site prediction
- see also DNA; Rad‐Seq; RNA‐Seq
- number of combined iterations
- oligo(s)
- in PCR primer design
- analysis
- internal
- in quality checking of designed primer
- restriction enzyme site detection
- OligoAnalyzer
- Oligonucleotide Properties Calculator
- omics
- one‐color microarray
- One to Three
- online/internet (incl. web resources)
- alignment tools
- books
- genome annotation
- Mendelian inheritance in animals and man
- microRNA
- in PCR primer design
- quality checking of designed primer
- protein structure (and its) prediction
- databases
- secondary
- tertiary
- restriction enzyme site detection
- SNP
- Website Search (NCBI)
- Online Biology Book
- ontology, gene (GO)
- open reading frames (ORFs)
- BLASTx and
- restriction enzyme site detection
- tBLASTn and
- operational taxonomic unit
- in Fitch–Margoliash algorithm
- in maximum parsimony method
- ORFs see open reading frames
- Organism
- in BLASTp
- in BLASTx
- in genome annotation in eukaryotes
- in Primer‐BLAST design
- in tBLASTn
- in tBLASTx
- in translation initiation site prediction
- outgroup (taxa)
- quality information/data (and its assessment)
- in differentially‐expressed gene identification
- in primer designing
- in tertiary protein structure prediction
- quantification/quantitation
- of gene expression with real‐time qPCR
- of reads mapping to known miRBase precursors, fst
- query coverage
- “Quick guide to sequenced genome”
- R package
- Rad‐Seq in SNP mining
- radiation tree
- Ramachandran plot
- Random Coding DNA
- Random DNA Sequence, DNA
- Range Extractor DNA and protein in sequence analysis
- RaptorX
- RasMol
- raw alignment score
- reads
- per kilobase (RPKM)
- per million mappable reads (RPKM)
- of miRNA
- fast quantification to known miRBase precursors
- preprocessing of
- processing of
- ReadSeq
- real‐time PCR see polymerase chain reaction
- receptor, ligand binding to (=docking)
- rectangular tree
- reference‐based methods
- sequence alignment
- SNP mining
- reference design in microarray data analysis of gene expression
- reference genes and genome
- Reference Sequence Database (RefSeq)
- reference transcriptome
- RefSeq see Reference Sequence Database
- RefSeqGene
- rendering control (RasMol)
- repeat hybridizations in microarray data analysis of gene expression
- repeat sequences (sequence repeats)
- dot plot analysis in identification of
- in PCR primers
- simple, in silico mining
- replicates in microarray data analysis of gene expression
- Representational State Transfer (REST)
- Research Collaboratory for Structural Bioinformatics (RSCB)
- Protein Databank (RCSB‐PDB)
- REST (Representational State Transfer)
- restriction enzymes
- mutations affecting digestion
- sites
- detection
- online resources
- in PCR primers
- Restriction Summary program
- Restriction Mapper
- Retrovirus Resources
- Reverse Complement
- Reverse Translate
- ribonuclease, bovine pancreatic
- ribonucleic acid see RNA
- ribosomal RNA (rRNA) database
- Rich Sequence Format (rsf) Format
- RNA, databases
- non‐coding
- sequence alignment
- sequence format conversion
- sequence statistics
- sequence translation
- mRNA(messenger RNA)
- miRNA(microRNA)
- database
- estimating expression of
- identification of known and novel miRNAs
- online resources
- target prediction
- rRNA
- RNA‐Seq
- root (and rooted tree)
- converting unrooted tree into
- interpretation of phylogenetic trees
- maximum parsimony method
- neighbor‐joining method
- unweighted‐pair group method with arithmetic
- RPKM (read per kilobase of exon per million mappable read)
- RSEM
- DE (differential expression) packages
- rsf (Rich Sequence Format) Format
- SAM/SAM files (sequence alignment maps)
- differential gene expression
- RNA‐Seq data analysis
- SNP mining
- SAMtools
- differential gene expression
- SNP mining
- SARS–CoV
- SCOP (Structural Classification of Protein) SCOP2
- search builder (nucleotide advanced), in nucleotide sequence retrieval from NCBI nucleotide database
- secondary structure
- Secure File Transfer Protocol (SFTP)
- seed–extend approach
- self‐complementarity (PCR primer)
- self‐dimers (homodimers)
- Seqret (EMBOSS)
- Sequence (ENA database)
- sequence(s) (biological/molecular)
- alignments see alignments
- dot plot analysis
- formats
- conversion
- important ones
- sequence box
- in designed primer quality checking, box
- in nucleotide sequence analysis
- Sequence Constructed (ENA database)
- Sequence Constructed expanded (ENA database)
- Sequence Manipulation Suite (SMS)
- Sequence Read Archive (SRA)
- sequence tags
- Sequence Version Archive (ENA database)
- sequencing
- sex‐determining region (SRY)
- SFTP
- SGT (Structural Genomics Targets)
- sheep miRNA target prediction
- short‐reads
- Simple Object Access Protocol (SOAP)
- single nucleotide polymorphism (SNP) mining
- SITES table
- Smith–Waterman algorithm
- SOAP (Simple Object Access Protocol)
- sodium ion (Na+) concentration and PCR primer quality checking
- solvent accessibility (ACC)
- speciation
- splice variants and spurious amplification
- SRY see sex‐determining region
- SSH File Transfer Protocol (SFTP)
- Stacks (software) for SNP mining
- star decomposition method
- star tree
- start codon (for translation)
- initiation site prediction
- PCR primer
- Stats
- stem‐loop see hairpin
- stop codon
- straight tree
- Structural Classification of Protein (SCOP) and SCOP2
- Structural Genomics Targets (SGT)
- Structure (Molecular Modeling Database)
- structure of proteins see proteins
- substitutions (base/nucleotide or amino acid)
- in evolutionary models of molecular phylogeny
- in maximum parsimony method, scoring for
- transitional
- transversional see transversions
- subtree
- SWISS‐MODEL
- SwissDock
- Swiss‐Prot
- SYBR green chemistry for real‐time PCR
- T cell receptor database
- T‐Coffee (e‐based Consistency objective function for alignment evaluation)
- Tajima–Nei + Gamma model
- TaqMan
- target‐template alignment view
- TargetScan
- taurine cattle see bovines
- taxon (taxa)
- evolutionary relationship among see evolution, relatedness
- outgroup
- in phylogenetic tree construction
- Fitch–Margoliash algorithm
- MEGA7
- minimum evolution method
- neighbor‐joining method
- unweighted‐pair group method with arithmetic mean
- in phylogenetic tree interpretation
- taxonomy
- tBLASTn
- tBLASTx
- TCP (Transmission Control Protocol)
- technical replicates in microarray data analysis of gene expression
- terminal nodes
- Terragenome
- tertiary structure (of protein)
- third party annotation
- threading method of tertiary protein structure recognition
- 3' end of PCR primers
- self‐complementarity
- stability
- SYBR green chemistry of qPCR
- threshold cycle (Ct), real‐time PCR data analysis
- threshold value see E‐value
- TIS Miner
- TMM (trimmed mean of M value)
- topology
- construction for sequences in maximum parsimony method
- torsion angles
- TPM (transcripts per million)
- Trace Archive
- trace‐back step
- Needleman–Wunsch algorithm
- Smith–Waterman algorithm
- Trans Extractor
- Accession Number
- EMBL
- GenBank
- Transcript (Ensembl)
- transcription
- gene prediction in transcripts
- transcription factor binding sites
- see also mRNA (look under RNA)
- transcriptome
- reference
- whole transcriptome shotgun sequencing (=RNA‐Seq)
- Transcriptome Shotgun Assembly (TSA) proteins
- TRANSFAC
- transitions (base)
- translated BLASTn (tBLASTx)
- translated BLASTx (tBLASTx)
- translation
- EMBOSS tools
- initiation site prediction
- Reverse Translate
- Translation Map
- Transmission Control Protocol (TCP)
- transversions (base)
- tree (phylogenetic)
- circular
- components
- see also specific components
- construction methods
- Fitch–Margoliash (FM) algorithm
- maximum parsimony (MP) method
- MEGA7 method
- minimum evolution (ME) method
- neighbor‐joining method
- unweighted‐pair group method with arithmetic mean
- horizontal dimensions
- inferring
- interpretation
- Fitch–Margoliash tree
- maximum parsimony tree
- MEGA7 tree
- minimum evolution tree
- neighbor‐joining tree
- unweighted‐pair group method with arithmetic mean tree
- maximum likelihood (ML)
- radiation
- rectangular
- representation
- rooted see root
- straight
- ultrametric see ultrametric tree
- understanding
- unrooted
- vertical dimensions
- Tree‐based Consistency objective function for alignment evaluation (T‐Coffee)
- TrEMBL
- trimmed mean of M value (TMM)
- tumor cells
- tutorials, online
- two‐color microarray
- UCSC see University of California at Santa Cruz
- ultrametric tree/data
- differentiation from non‐ultrametric data
- see also dendrogram
- UnaFold
- Uncultured/environmental sample sequences
- BLASTp
- BLASTx
- primer‐BLAST
- tBLASTx
- tLASTn
- UniGene
- UniParc
- UniProt Reference Clusters
- UniProtKB
- UniSTS
- United States Patent and Trademark Office (USPTO) Proteins
- University of California at Santa Cruz (UCSC)
- chimera tool (tool for structure visualization)
- genome browser
- unrooted tree
- conversion into rooted tree
- unweighted‐pair group method with arithmetic mean (UPGMA)
- USPTO (United States Patent and Trademark Office) Proteins
- Variant Call Format (VCF)
- VCF (Variant Call Format)
- Viral Genome (NCBI database)
- virus, gene finding
- Virus Variation (NCBI database)
- Web Map
- web resources see online
- WEBcutter
- weighted‐pair group method with arithmetic mean (WPGMA)
- weighted parsimony
- WHAT IF
- whole genome shotgun contigs
- whole transcriptome shotgun sequencing (=RNA‐Seq)
- window size in dot plot analysis
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