Background frequencies for residue variability estimates: BLOSUM revisited by Reš I, Mihalek I, Lichtarge O

“…To do that, we revisit the original construction of BLOSUM matrices, and re-interpret them as mutation probability matrices. …”
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RBLOSUM performs better than CorBLOSUM with lesser error per query by Renganayaki Govindarajan, Biji Christopher Leela, Achuthsankar S. Nair

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Accurate prediction of immunoglobulin proteins using machine learning model by Ali Ghulam, Rahu Sikander, Farman Ali, Zar Nawab Khan Swati, Ahsanullah Unar, Dhani Bux Talpur

“…The value of the BLOSUM62 Matrix is determined through a large-scale analysis of observed polypeptide alignments. …”
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A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships by Lemaitre Claire, Barré Aurélien, Citti Christine, Tardy Florence, Thiaucourt François, Sirand-Pugnet Pascal, Thébault Patricia

“…Our approach is inspired from the one used to build the BLOSUM matrices and is based on learning substitution and amino acid frequencies on real sequences with the corresponding compositional bias. …”
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A novel series of compositionally biased substitution matrices for comparing <it>Plasmodium </it>proteins by Pizzi Elisabetta, Brick Kevin

“…<p>Abstract</p> <p>Background</p> <p>The most common substitution matrices currently used (BLOSUM and PAM) are based on protein sequences with average amino acid distributions, thus they do not represent a fully accurate substitution model for proteins characterized by a biased amino acid composition. …”
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A study on biomolecular sequence alignment using machine learning techniques by Othman, Muhamad Razib, Salim, Naomie, Abdul Jalil, Rozita, Deris, Safaai, Mat Yatim, Safie, Md. Illias, Rosli

“…Substitution matrices that will be used are BLOSUM45, BLOSUM62 and BLOSUM80. While linear gap penalty with range values parameter from (–d=1 to –d=10) or affine gap penalty with range values parameter for opening gap from (–d=1 to –d=12) and extension gap from (–e=1 to–e=5). …”
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Multiple sequence aligment menggunakan hidden Markov model dengan augemented set dan pengaruhnya terhadap akurasi pohon filogenetik by AFIAHAYATI, AFIAHAYATI

“…There are two kind of m utation process, first based on substitution matrix BLOSUM 80 and second, random mutation. Augmented set used as input into the HMM to obtain the MSA. …”

Finding the best biological pairwise alignment through genetic algorithm by Carlos Dias Maciel, Ailton Akira Shinoda, Paulo Mologni

“…Each chromosome is associated with a fitness function based on BLOSUM50 substitution matrix.…”
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PFASUM: a substitution matrix from Pfam structural alignments by Frank Keul, Martin Hess, Michael Goesele, Kay Hamacher

“…PFASUM matrices with comparable relative entropies to the commonly used substitution matrices BLOSUM50, BLOSUM62, PAM250, VTML160 and VTML200 outperformed their corresponding counterparts in 93% of all test cases. …”
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Determinando o melhor alinhamento biológico através do algoritmo genético by Paulo Mologni, Ailton Akira Shinoda, Carlos Dias Maciel

“…O cromossomo está associado a uma função objetivo dependente da matriz de substituição BLOSUM50.…”
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Novel Method of 3-Dimensional Graphical Representation for Proteins and Its Application by Zhao-Hui Qi, Ke-Cheng Li, Jin-Long Ma, Yu-Hua Yao, Ling-Yun Liu

“…In this article, we propose a 3-dimensional graphical representation of protein sequences based on 10 physicochemical properties of 20 amino acids and the BLOSUM62 matrix. It contains evolutionary information and provides intuitive visualization. …”
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Data on the sequence-derived properties of gastric cancer – binding peptides by Jose Isagani B. Janairo, Marianne Linley L. Sy-Janairo

“…The nine calculated sequence-derived descriptor classes are the Blosum indices, Cruciani properties, FASGAI vectors, Kidera factors, ProtFP, ST-scales, T-scales, VHSE scales, and Z-scales. …”
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Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors by Zimmermann Karel, Gibrat Jean-François

“…We also characterize and compare the PAM and BLOSUM series substitution matrices.</p> <p>Conclusions</p> <p>This vector encoding introduces a Euclidian metric in the amino acid space, consistent with substitution matrices. …”
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Interpreting missense mutations in Human TRIM5alpha by computational methods by Chan Philip A

“…The four comparative method programs assessed included SIFT, PolyPhen, A-GVGD, and average BLOSUM62 pairwise score. Two common polymorphisms, H43Y and R136Q, were predicted to be benign based on comparative sequence analysis. …”
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Characterization, Identification and Phylogeny of the Cretaine Kinase (ckma) Gene in Medaka (Oryzias latipes) by Mehtap BAYIR, Gökhan ARSLAN, Pinar OĞUZHAN YILDIZ

“…In this study, characterization and identification, phylogenetic relationship, conserved gene synteny of ckma gene in medaka (O. latipes) which is an important model organism were analyzed by using bioinformatics tools (NCBI database, Ensembl genomic database, Expasy, Reverse Complementary and some programs such as MEGA6 program, BLOSUM62 matrix program and BioEdit software). All these data will be used in future studies on molecular stress response in fish and they were presented to the scientific world with this study.…”
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Amino acid properties conserved in molecular evolution. by Witold R Rudnicki, Teresa Mroczek, Paweł Cudek

“…Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. …”
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Optimizing amino acid substitution matrices with a local alignment kernel by Vert Jean-Philippe, Saigo Hiroto, Akutsu Tatsuya

“…The local alignment kernel depends on an amino acid substitution matrix. Since commonly used BLOSUM or PAM matrices for scoring amino acid matches have been optimized to be used in combination with the Smith-Waterman algorithm, the matrices optimal for the local alignment kernel can be different.…”
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Reticular alignment: a progressive corner-cutting method for multiple sequence alignment. by Szabó, A, Novák, A, Miklós, I, Hein, J

“…Reticular Alignment can outperform ClustalW even if a very simple scoring scheme (BLOSUM62 and affine gap penalty) is implemented and merely the threshold value is increased. …”

Conservation of amino acids in multiple alignments: aspartic acid has unexpected conservation by Fiser, A, Simon, I, Barton, G

“…Analysis of recently derived substitution matrices (e.g. BLOSUM) confirms that Glu tends to substitute more frequently with other amino acids than does Asp. …”

Structural homology of metal-dependent proteins of woody plants used in agroforestry of arid areas by Krylov Pavel A., Tretyakova Anna V.

“…Bioinformatic analysis included multiple alignment of amino acid sequences using the Ugene program by the ClustalW algorithm (BLOSUM62 matrix). According to the results of studying the plants metalloproteome, it was found that Quercus robur has 18 proteins, Robinia pseudoacacia – 24, Gleditsia triacanthos – 3, Ulmus pumila – 19, Fraxinus excelsior – 14 metal-dependent proteins. …”
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