Methods and algorithms for statistical analysis of protein sequences.

Abstract

We describe several protein sequence statistics designed to evaluate distinctive attributes ofresidue content and arrangement in primary structure. Considered are global compositional biases, local clustering of different residue types (e.g., charged residues, hydrophobic residues, Ser/Thr), long runs of charged or uncharged residues, periodic patterns, counts and distribution of homooligopeptides, and unusual spacings between particular residue types. The computer program SAPS (statistical analysis of protein sequences) calculates all the statistics for any individual protein sequence input and is available for the UNIX environment through electronic mail on request to V.B. (volker@gnomic.stanford.edu).Newly derived protein sequences are commonly subjected to standard sequence analysis involving identification of similarities to other proteins in data bases, prediction of secondary structure, hydropathy plots, and mapping of potential glycosylation and phosphorylation sites and other motifs (see, e.g., refs.

Isolation and Characterization of the cDNA Encoding Bovine Poly(ADP-ribose) Glycohydrolase

“…We have noted that the expressed PARG protein can form dimers stable to SDS-PAGE conditions. In that regard, residues 871-907 show significant homologies to known leucine zipper dimerization sequences (48). Another motif identified is a putative bipartite nuclear location signal (NLS) (49).…”

The Candida albicans CTR1 gene encodes a functional copper transporter

“…Analysis of the C. albicans CTR1 protein sequence using the SAPS analysis program (http://www.isrec.isb-sib.ch/software/ SAPS_form.html; Brendel et al, 1992) revealed a predicted protein of 251 amino acids with a molecular mass of 27?8 kDa, lacking an amino-terminal leader sequence. Dancis et al (1994a) previously reported that S. cerevisiae Ctr1p has a methionine-and serine-rich amino-terminal region that contains a putative copper-binding domain.…”

Protein and lipid oxidative damage and complex I content are lower in the brain of budgerigar and canaries than in mice. Relation to aging rate

“…Quantification was performed by using standard curves for each amino acid, and results recalculated to be expressed as mol%. The following indices from amino acid compositional analysis were also calculated: KR (Lys + Arg): positive charge; ED (Glu + Asp): negative charge; KR + ED: total charge; KR-ED: net charge; LVIFM (Leu + Val + Ile + Phe + Met): major hydrophobics; and the groupings AGP (Ala + Gly + Pro) (encoded by CCN, GCN, and GGN codons), and FIKMNY (Phe + Ile + Lys + Met + Asn + Tyr) (encoded by AAN, AUN, UAN, and UUN codons), according to Brendel et al (Brendel et al 1992). …”