| Title | Bioinformatics: symbol comparison tables and protein sequences | |
| Authors | Vassiliki-Sofia Grech¹, Maria Grech², Antonios Togias³ and Ioanna Grech⁴
1. Bachelor of Medical Biochemistry, King’s College University, Student of Medicine, Medical University of Pecs, Hungary 2. Medical Resident in Pediatrics, Children’s Hospital Aglaia Kyriakou, Athens, Greece 3. Medical Resident in Pediatrics, General Hospital of Kalamata 4. Technological Education Institution of Athens, Egaleo, Athens, Greece |
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| Citation | Grech, V.S., Grech, M., Togias, A., Grech, I.: Bioinformatics: symbol comparison tables and protein sequences, Epitheorese Klin. Farmakol. Farmakokinet. 25(3): 115-123 (2011) | |
| Publication Date | Accepted for publication: November 10, 2011 | |
| Full Text Language | English | |
| Order – Buy | Ηλεκτρονική Μορφή: pdf (10 €) – Digital Type: pdf (10 €)
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| Keywords | Protein sequences, symbol comparison tables, scoring matrices, alignments, 2D structure of proteins. | |
| Other Terms | review article | |
| Summary | Analysis of protein sequence alignment can enable the connection between different amino acids and providing important information of their evolutionary pattern. Scientists can answer questions related to human origin and genetic similarities among organisms, even create model organisms. Nevertheless, this is not a simple process and number of difficulties like sequence mutations and the huge number of alignments, are to overcome. In order to study these sequences, symbol comparison tables were created, based on statistical methods. They are used as scoring matrices for computing alignment scores, comparing any two amino acid sequences. One of the first attempts for matrixes formation is the Unitary Protein Matrix (UPM). Another simple symbol comparison table is the Genetic Code Matrix (GCM), and a third one is called Structure Genetic Matrix (SGM), published in 1972 by McLachlan. However, groupings used for the observations are artificial. For that reason, there is no assurance that a random common amino acid property is significant for functional and structural relationships between amino. The most extensively used symbol comparison tables are the Log Odd Matrix (LOM), the very similar Mutation Data Matrix (MDM) known also as Accepted Point Mutation (PAM) designed by Dayhoff in1978, Perwise Exchange Table 1991 (PET1991) created by Jones et al. at 1992 and Blocks of amino acid Substitution Matrix (BLOSUM) designed by S. & J. Henikoff in 1992. Moreover, all the pure systemized mathematical techniques do not apply directly to the natural word. Natural selection and relative mutability had to be taken into account, as well as relative mutability had to be normalized. In addition, global and local alignments are used. Local alignments, on the one hand, used mainly by BLOSUM, use part of a sequence in order to compare two amino acids. Consequently, they are more useful for dissimilar series believed to enclose regions of similarity or similar sequence motifs. Global alignments, on the other, use the whole sequence in order to align every residue in every sequence and are more useful when the sequences are closely related. PAM matrices are entrenched in global alignments of sequences being more than 85% identical. Last but not least, alignments may not be biologically significant by themselves, but through comparison tables are able to provide statistical information, reflecting structural equivalent positions in aligned families of protein. This can be the starting point for the de novo prediction of secondary protein structures. | |
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Online ISSN 1011-6575
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Articles published in this Journal are Indexed or Abstracted in: • Chemical Abstracts • Elsevier’s Bibliographic Databases: Scopus, EMBASE, EMBiology, Elsevier BIOBASE SCImago Journal and Country Rank Factor
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