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In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format allows for sequence names and comments to precede the sequences.
The peptide sequence of the myc-tag is (in 1- and 3-letter codes, respectively): EQKLISEEDL and Glu-Gln-Lys-Leu-Ile-Ser-Glu-Glu-Asp-Leu. The tag is approximately 1202 daltons in atomic mass and has 10 amino acids. It can be fused to the C-terminus and the N-terminus of a protein.
3- and 1-letter symbols Side chain Hydropathy index [50] Molar absorptivity [51] Molecular mass Abundance in proteins (%) [52] Standard genetic coding, IUPAC notation; 3 1 Class Chemical polarity [53] Net charge at pH 7.4 [53] Wavelength, λ max (nm) Coefficient ε (mM −1 ·cm −1) Alanine: Ala A Aliphatic Nonpolar Neutral 1.8 89.094 8.76 ...
S-tag is the name of an oligopeptide derived from pancreatic ribonuclease A (RNase A).. If RNase A is digested with subtilisin, a single peptide bond is cleaved, but the resulting two products remain weakly bound to each other and the protein, called ribonuclease S, remains active although each of the two products alone shows no enzymatic activity.
A consensus logo is a simplified variation of a sequence logo that can be embedded in text format. Like a sequence logo, a consensus logo is created from a collection of aligned protein or DNA/RNA sequences and conveys information about the conservation of each position of a sequence motif or sequence alignment [1] [4].
Either a three letter code or single letter code can be used to represent the 22 naturally encoded amino acids, as well as mixtures or ambiguous amino acids (similar to nucleic acid notation). [1] [2] [3] Peptides can be directly sequenced, or inferred from DNA sequences. Large sequence databases now exist that collate known protein sequences.
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Proteins may be classified as to their three-dimensional structure (also known a protein fold). The two most widely used classification schemes are: [2] CATH database [3] Structural Classification of Proteins database (SCOP) [4] Both classification schemes are based on a hierarchy of fold types.