Chemical & Biomolecular Formats

Mathematica can import—and often export—standard formats used in chemistry, molecular biology and bioinformatics, routinely handling a full range of molecular types, as well as genome-sized datasets.

ReferenceReference

Chemical Formats

"XYZ" XYZ molecule geometry file (.xyz)

"MOL" MDL MOL format (.mol)

"MOL2" Tripos MOL2 format (.mol2)

"SDF" MDL SDF format (.sdf)

"SMILES" SMILES chemical format (.smi)

"HIN" HyperChem molecular data format (.hin)

"JCAMP-DX" chemical spectroscopy format (.jdx, .dx, .jcm)

Bioinformatics Formats

"GenBank" NCBI GenBank sequence format (.gb, .gbk)

"FASTA" DNA, RNA, and amino acid sequence format (.fasta, .fa, .fsa, .mpfa)

"FASTQ" DNA and RNA sequence format with base qualities (.fastq, .fq)

"NEXUS" NEXUS phylogenetic data format (.nex, .ndk)

"AgilentMicroarray" microarray data format (.txt)

"Affymetrix" microarray data format (.cel, .cdf, .chp, .gin, .psi)

"SFF" DNA sequence flowgram format (.sff)

Molecular Biology Formats

"PDB" Protein Data Bank format (.pdb)

"MMCIF" MMCIF 3D molecular model format (.cif)

"FCS" flow cytometry data format (.fcs, .lmd)

Common Elements

chemical structure diagram

3D molecular graphics

3D coordinates of atoms

base-pair or amino acid sequence

all available elements

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