Basic Applied Bioinformatics

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)
  • dot plot analysis
  • global see global alignment
  • local see local alignment
  • MEGA7
  • multiple see multiple sequence alignments
  • online tools
  • pairwise see pairwise sequence alignment
  • protein see proteins
  • raw (score)
  • Ref‐Seq
  • target‐template
  • see also BAM; Genomic Mapping and Alignment Program; SAM
• 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
  • substitution see substitution
• 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
  • functional see functional annotation
  • genome see genome
  • third party
• Antisense Design, IDT
• Arabidopsis thaliana miRNA targets
• archaea gene finding
• arithmetic mean
  • definition
  • unweighted‐pair group method with (UPGMA)
  • weighted‐pair group ...