Protein database searches using compositionally adjusted substitution matrices

By Stephen F. Altschul, John C. Wootton, E. Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schäffer, Yi-Kuo Yu. 2005

1,094 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

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Citations in the corpus

Accelerated Profile HMM Searches (2011, background): “Biased composition correction has received close attention in NCBI BLAST software development [7,8,42], but is not part of the textbook description of ‘‘optimal’’ Smith/Waterman local alignment.”
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids (2010, methodology): “(2) Homologous sequences are collected using a BLAST (or PSI-BLAST) (6,7) search against a selected database.”
RiceXPro Version 3.0: expanding the informatics resource for rice transcriptome (2012, methodology): “This search function allows users to extract a gene/genes by BLAST search options (34,35), namely, blastn, tblastn and tblastx against coding sequence of genes with probes in the Rice 4x44K Microarray platform (Figure 3).”
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis (2009, methodology): “Compositional adjustment (28,29) is applied, as is the SEG low-complexity filter (30), set so as to mask only during seeding but not during extension (soft masking).”
Sensitive protein alignments at tree-of-life scale using DIAMOND (2021, methodology): “24 ).”
SIMAP—the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage (2013, methodology): “Furthermore, we have already planned to increase the sensitivity and accuracy of the SIMAP matrix using composition-based score adjustment (33,34) that is so far not used in SIMAP and will switch from FASTA (18) search heuristics fully to the non-heuristic Smith–Waterman algorithm (19).”
Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: structure and function of a large, enigmatic family. (2010, background): “GH61 proteins detected by BLAST (30, 31) searching of the Uniprot (32) and GENESEQ (Thomson Reuters Corp.) databases were aligned Table 1: Data Collection (100 K) and Other Statistics for the GH61E Structuresa data set native K2Au(CN)2 PHMBS ZnSO4 data collection space group F23 F23 F23 F23 cell dim”
Protein sequence design with a learned potential (2020, methodology): “To conﬁrm that key sequence features are retained despite the increased variability seen, we calculated Psipred [75, 76, 77, 78, 79, 80] secondary structure prediction cross-entropy relative to DSSP assignments [81].”
The Role of Balanced Training and Testing Data Sets for Binary Classifiers in Bioinformatics (2013, methodology): “From the position-specific scoring matrices (PSSMs) output by PSI-BLAST, we obtained the dPSSM score PLOS ONE | www.plosone.org 2 July 2013 | Volume 8 | Issue 7 | e67863 which is the difference between the PSSM score of the wildtype residues and the PSSM scores of the mutant residues.”
Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone (2011, methodology): “The first line contains the protein name or PDB-id and BLAST E-value to the query (plus query name), where appropriate.”
NCBI BLAST: a better web interface (2008, methodology): “(4) The Alignments section presents the alignments of the HSPs, either as a series of pairwise alignments (default), or as a single block of all HSPs anchored to the query.”
eggNOG v4.0: nested orthology inference across 3686 organisms (2013, methodology): “The alignments and scores between all homologous protein pairs are, therefore, recalculated using low-complexity masking and with compositional adjustment of the amino acid substitution matrix (43) to account for compositional biases and low-complexity regions.”