Statistics of Local Complexity in Amino Acid Sequences and Sequence Databases

By John C. Wootton, S. Federhen. 1993

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Citations in the corpus

Flexible sequence similarity searching with the FASTA3 program package. (2000, methodology): “elegans collagen or ssggvtfsvss from a Drosophia trypsin) in the query sequence (3, 14).”
Recent progress in protein subcellular location prediction. (2007, methodology): “To get the desired results, the sequence similarity search-based tools, such as BLAST [45,46], usually are used to conduct the prediction.”
The human gene damage index as a gene-level approach to prioritizing exome variants (2015, methodology): “We calculated proteins complexity by first extracting the amino acid sequences corresponding to the proteins (27, 28) and then estimating the relative amino acid composition complexity using Clark ’ s distance (63, 64).”
Illuminating protein space with a programmable generative model (2022, methodology): “The score used in the annealing was the Potts energy plus a flat-bottom restraint energy around the sequence complexity calculated as equation 4 in [Wootton and Federhen, 1993].”
De novo identification of repeat families in large genomes (2005, methodology): “Repeat families with >50% of their length annotated as low-complexity by Nseg (Wooton and Federhen, 1993) were removed.”
Protein secondary structure prediction based on position-specific scoring matrices. (1999, methodology): “This databank, which currently contains around 340,000 sequences, is then ®ltered with the SEG program (Wootton & Federhen, 1993) to remove regions with very low information content.”
iSNO-PseAAC: Predict Cysteine S-Nitrosylation Sites in Proteins by Incorporating Position Specific Amino Acid Propensity into Pseudo Amino Acid Composition (2013, methodology): “To identify its attribute, the tools for computing amino acid sequence similarity, such as BLAST [26,27], were utilized to search the database for those targets that have high sequence similarity to the query protein or peptide.”
CIDER: Resources to Analyze Sequence-Ensemble Relationships of Intrinsically Disordered Proteins (2017, background): “The linear sequence complexity can be calculated using one of three possible complexity measures, viz., Wootton-Federhen complexity (21), linguistic complexity (22), and Lempel-Ziv-Welch complexity (23).”
Human non-synonymous SNPs: server and survey. (2002, methodology): “Protein sequences and genomic fragments were preprocessed with the SEG (16), XNU (17), RepeatMasker (18)”