Index

    • 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
    • [AG]XXATGC
    • 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
    • BLAST
    • BLASTn
      • translated (tBLASTn)
    • 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
      • long branch attraction
    • 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
      • delta
    • 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
      • miRNAs
    • 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
        • microarrays
        • packages
    • dihedral angle
    • Discontiguous MegaBLAST
    • distance (values)
      • global distance test
      • in neighbor‐joining method
        • new
      • pairwise
      • in unweighted‐pair group method with arithmetic mean
    • distance matrix
      • in minimum evolution method
      • in neighbor‐joining method
        • with internal node
        • new
      • in unweighted‐pair group method with arithmetic mean
    • distance scale
    • divalent cations in PCR primary design
    • divergence
      • mean
      • net
    • DNA
      • amplification
        • bridge amplification
        • efficiency (in RT‐qPCR)
        • by PCR see polymerase chain reaction
        • phases (in RT‐qPCR)
        • spurious, detecting
      • 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)
      • BLASTn
    • 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)
      • Seqret
    • ENA (European Nucleotide Archive)
    • energy functions
    • Ensembl
      • databases
      • IDs
    • 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)
      • database of (dbEST)
    • external nodes
    • F81 model
    • FACTORS table
    • FASTA (fast all)
      • in BLASTn
      • in BLASTp
      • Combine
      • in differential gene expression
        • eukaryotes
      • in genome annotation
        • eukaryotes
        • prokaryotes
      • 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
      • EMBL
      • GenBank
    • 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
        • SYBR
    • FMTSeq
    • fold change (in gene expression)
    • fold recognition (=threading method)
    • FPKM (fragment per kilobase of exon per million mappable reads)
    • free energy
      • Gibbs (ΔG)
        • in molecular docking
    • 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
      • annotation
    • Genome Analysis Toolkit (GATK)
    • Genome (NCBI database)
    • Genome Reference Consortium
    • Genome Survey Sequence (dbGSS)
    • Genome Survey Sequences (GSS)
      • database (dbGSS)
    • 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)
      • max HMM iterations
    • 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
      • simple sequence repeats
    • InDel and Indels see insertion and deletion
    • Influenza Virus (NCBI database)
    • insertion and deletion(s) (InDel and Indels)
      • in dot plot analysis
    • 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
      • amino acid
      • nucleic acid
    • internet see online
    • InterPro
      • Matches Complete
    • introns
      • BLASTn
      • in genome annotation
        • eukaryotes
        • prokaryotes
    • 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)
    • β‐lactoglobulin
    • LALIGN
    • leaf (leaves)
    • least‐distant pair
    • libraries
      • binding site searches
      • differentially expressed genes
        • DESeq2 and
        • edgeR and
      • PCR primer design
    • 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
      • Discontiguous
    • MEGAN 4 (MEtaGenome ANalyzer)
    • melting temperature (Tm) of PCR primers
      • mismatch
      • optimal
    • Mendelian Inheritance (Online)
      • in Animals
      • in Man
    • 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)
      • DNA
      • protein
    • 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
        • maximum parsimony method
    • Multiple Sequence Comparison by Log‐Expectation (MUSCLE)
    • MUSCLE (Multiple Sequence Comparison by Log‐Expectation)
    • Mutate DNA
    • Mutate for Digest
    • MUTATE Protein
    • mutations
      • rate
    • Mview
    • c‐MYC
    • National Center for Biotechnology Information (NCBI)
      • 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
        • eukaryotes
        • prokaryotes
      • 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
        • eukaryotes
        • prokaryotes
      • 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)
    • paired‐end sequencing
    • pairwise distances
    • pairwise sequence alignment
      • BLASTn
      • BLASTx
      • EMBL database
      • RNA‐Seq data analysis
      • SWISS‐MODEL program
      • tBLASTn
      • tBLASTx
    • pairwise test for differential expression between two groups
    • palindrome
    • pancreatic ribonuclease, bovine
    • paraphyletic group
    • parsimony
      • maximum (MP method)
      • transversion (T‐P)
      • weighted
    • patents
      • DNA
      • proteins
    • Pattern Find
      • DNA
      • protein
    • PDB (RSCB Protein Data Bank)
    • Pearson/FASTA format
    • Perl
    • Pfam
    • phages, gene finding
    • phenetic methods of tree construction
    • phenogram
    • Phenotypes, database of Phenotypes and (dbGaP)
    • phi‐angle
    • PHI‐BLAST (Position Hit Initiated)
    • phred scale
    • PHYLIP
      • format
    • phylogeny (molecular)
      • basis
      • databases
      • evolution and models of
      • morphology‐based
      • test of
      • tree see tree
    • phylogram
    • Picard tools
    • PIR (Protein Information Resource)
    • plants, small RNA target analysis
    • plasmid(s), gene finding
    • Plasmid Vectors (NebCutter)
    • pocket multiplicity
    • point mutations
    • Poly(A) Signal Miner
    • polymerase chain reaction (PCR)
    • polyphyletic group
    • PopSet
    • Position Hit Initiated BLAST (PHI‐BLAST)
    • Position‐Specific Iterative‐BLAST (PSI‐BLAST)
      • secondary protein structure prediction using (PSIPRED)
    • position‐specific scoring matrix (PSSM)
    • position weight matrices
    • primary structure (protein/polypeptide)
    • primer(s) (for PCR)
      • definition
      • designing
        • online resources see online
        • quality checking of designed primers
      • pairs
        • melting temperature mismatch
        • selection of best pairs
    • Primer3
    • primer‐BLAST
    • PRINSEQ
    • probe (for microarray)
    • Probe (NCBI database)
    • prokaryotic gene annotation
    • PROSITE
    • protein(s)
      • alignment
        • BLAST search tools
        • RaptorX
      • allosteric
      • in BLASTp search‐sets
      • comparative modeling
      • databases
        • functional analysis
        • RefSeq
      • families
      • filter
      • fold recognition (=threading method)
      • isoelectric point
      • ligand binding to (=docking)
      • Molecular Weight
      • MUTATE Protein
      • patented
      • Pattern Find
      • Range Extractor
      • Stats
      • structure
    • Protein Clusters (NCBI database)
    • Protein Data Bank (of Research Collaboratory for Structural Bioinformatics; RSCB‐PDB)
    • Protein Database (NCBI)
    • Protein Information Resource (PIR)
    • proteomics
    • Protocol Online
    • Protocols in Cytogenetics
    • pseudo count
    • psi angles
    • PSI‐BLAST see Position‐Specific Iterative‐BLAST
    • PSIPRED
    • psRNATarget
    • PubChemBioAssay
    • PubChemCompound
    • PubChemSubstance
    • PubMed
    • PubMed Central
    • PubMed Health
    • 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
      • BLAST
    • 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
        • using GATK
        • using STACKS
    • reference design in microarray data analysis of gene expression
    • reference genes and genome
      • sequences
    • Reference Sequence Database (RefSeq)
      • proteins
      • RNA
    • 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
        • humans
        • plants
    • rRNA
      • 18S
      • database
    • 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
      • PCR primers
        • amplicon
      • protein
        • prediction
    • 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)
      • taurine
    • SFTP
    • SGT (Structural Genomics Targets)
    • sheep miRNA target prediction
    • short‐reads
    • Simple Object Access Protocol (SOAP)
    • single nucleotide polymorphism (SNP) mining
      • online resources
    • 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
      • DNA
      • protein
    • stem‐loop see hairpin
    • stop codon
      • in‐frame
    • 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
      • pruning–regrafting (SPR)
    • 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)
      • prediction
    • 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)
      • parsimony (T‐P)
    • 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
      • Library Browser
    • 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
    • X‐ray crystallography
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