Position-based sequence weights.

By Steven Henikoff, Jorja G. Henikoff. 1994

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The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

1. Ben M. Webb
2. Narayanan Eswar
3. Andrej Sali
4. Yang Zhang
5. Jinbo Xu
6. Yoshua Bengio
7. Jimin Pei
8. Johannes Söding

Citations in the corpus

• Predicting functionally important residues from sequence conservation (2007, methodology): “We implemented the sequence weighting method proposed in Henikoff and Henikoff (1994) that rewards sequences that are ‘surprising’.”
• Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. (2001, methodology): “Thanks to Drs Jorja and Steven Henikoff for providing the frequency ratios used to derive the BLOSUM score matrices .”
• Comparative Protein Structure Modeling Using Modeller (2006, background): “The information in a multiple sequence alignment is most often encoded as either a position-specific scoring matrix (PSSM; Henikoff and Henikoff, 1994; Altschul et al., 1997) or as a Hidden Markov Model (HMM; Krogh et al., 1994; Eddy, 1998).”
• PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. (1999, methodology): “Sequence weights are calculated from a matrix of pairwise sequence–sequence similarities (Vingron and Sibbald, 1993) or from the amino acid type diversity observed at each alignment position (Henikoff and Henikoff, 1994).”
• Homology Detection via Family Pairwise Search (1998, unknown): “Such schemes may significantly improve the performance of homology detection algorithms (Altschul et al, 1989; Sibbald and Argos, 1990; Thompson et al, 1994); however, Henikoff and Henikoff ( 1994) have shown that many weighting schemes perform almost as well as one another.”
• Prediction of amino acid sequence from structure (2000, methodology): “As a control, we also collected profile statistics with sequence weighting incorporated to correct for biased sampling in the aligned sequences ~ Henikoff & Henikoff, 1994 !”
• A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety (2007, methodology): “Genes of similar length with over 60% of similarity alignments at protein level were considered homologous using BLOSUM62 matrix [123].”
• AL2CO: calculation of positional conservation in a protein sequence alignment (2001, methodology): “We used a modified method of Henikoff and Henikoff that is implemented in PSI-BLAST (Henikoff and Henikoff, 1994; Altschul et al., 1997).”
• Correlated mutations in models of protein sequences: phylogenetic and structural effects (1999, background): “Various attempts to "weight" sequences in a manner related to the tree to correct for bias exist in the literature [Altschul et al. (1989), Sibbald k Argos (1990), Gerstein et al. (1994), Hennikoff & Hennikoff (1994), Thompson et al. (1994)].”