Comparison of methods for searching protein sequence databases

By William R. Pearson. 1995

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Citations in the corpus

Hidden Markov model speed heuristic and iterative HMM search procedure (2010, methodology): “Parameter effects on runtime were determined by searching the models against a non-redundant version of NCBI’s NR database(NRDB90) and effects on sensitivity and specificity, as measured by minimum error rate (MER) [14] (See Methods), were determined by searching against our benchmarking database us”
Protein database searches using compositionally adjusted substitution matrices (2005, background): “The sensitivity of a protein database search can depend strongly on the choice of a substitution matrix [18,19].”
Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. (2004, methodology): “Among these were meth-ods proposed by Shpaer et al. (1996) and Pearson (1995, 1998), who used different kinds of ln/ln normalization, whereas Arslan et al. (2001) devised special, but even slower, iterated Smith-Waterman computational algorithms with fractional programming.”
PHAT: a transmembrane-specific substitution matrix (2000, methodology): “The relative entropy ( H) of a matrix is defi ned as the average information per aligned residue pair and is calculated by: H = � i� j q ij s ij . By comparing BLOSUM matrices to other matrices with similar relative entropy, it was shown that the BLOSUM series performed as well as or better than oth”
Homology Detection via Family Pairwise Search (1998, unknown): “In addition to ROC50 analysis, each homology detection method is evaluated using the equivalence number [34].”
A novel shape complementarity scoring function for protein‐protein docking (2003, methodology): “(P value) is less than 3 10 (5), computed using the sign test.(49) Judged by the rank of the first hit, PSC performed”
Query-Dependent Banding (QDB) for Faster RNA Similarity Searches (2007, methodology): “The minimum error rate (MER) (‘‘equivalence score’’) [38] was used as a measure of benchmark performance.”
Hidden Markov models for detecting remote protein homologies (1998, methodology): “The fourth test is Pearson's test for sequencecomparison tools Pearson, 1995.”
Test Collection Based Evaluation of Information Retrieval Systems (2010, background): “Note that at the point R, the number of relevant documents ranked below R will always equal the number of non-relevant documents ranked above R, which has led others to refer to R as the equivalence number and called R-precision missed@equivalent [189].”
Pcons: A neural‐network–based consensus predictor that improves fold recognition (2001, methodology): “(3) Methods using heuristic alignment techniques such as FASTA (Pearson and Lipman 1988; Pearson 1995) or BLAST2 (Altschul et al.”
PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. (1999, methodology): “Scores were normalized with the empirical model of Pearson (1995).”