Aaron's ArchiveDNA, RNA & protein toolkit

Aaron's Archive / Guides

Guides

Plain-language references for every tool: what it measures, how to read the result, and exactly how Aaron's Archive computes it. 12 guides, about 43 minutes in all.

Sequence basics

What a sequence contains and how to find genes in it.

GC ContentThe share of G and C bases: how to calculate it, what it tells you, and how to read GC skew.5 min readOpen Reading FramesHow genes are read in triplets, why a sequence has six reading frames, and how to judge an ORF.4 min read

PCR, cloning & editing

Designing primers, cutting DNA and choosing CRISPR guides.

Melting Temperature (Tm)What Tm is, three ways to estimate it, and why different calculators disagree.4 min readPrimer DesignThe rules of thumb for good PCR primers, and what hairpins and primer-dimers are.5 min readRestriction MappingHow restriction enzymes find their sites, what sticky and blunt ends are, and how to plan a cloning digest.4 min readCRISPR Guide DesignHow a guide RNA and a PAM direct Cas9 to a target, and how guides are chosen and scored.3 min read

Searching & comparing

Finding related sequences and measuring how similar they are.

BLAST SearchingHow BLAST finds related sequences, and how to read E-values, identity and coverage.3 min readSequence AlignmentGlobal vs local alignment, scoring matrices, gap penalties, and how to read identity.3 min readPhylogenetic TreesWhat a tree shows, how UPGMA builds one from distances, and what it assumes.3 min read

RNA & proteins

Folding RNA and reading protein properties.

RNA FoldingHow a single RNA strand folds on itself, what minimum free energy means, and how to read dot-bracket.3 min readProtein PropertiesWhat molecular weight, pI, GRAVY, instability index, aliphatic index and ε280 mean for experiments.3 min read

Mutations

Predicting what a change in DNA does to a protein.

Variant EffectsSilent, missense, nonsense and frameshift changes, how to write them in HGVS, and what Grantham distance says.3 min read

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