Benítez-Hidalgo, A., Roldán-García, M. M., & Navas-Delgado, I. (2021, September 14). SALON - Pairwise and Multiple Sequence ALignment ONtology. W3ID. https://w3id.org/salon 2020-11-01T23:59:59 10.5281/zenodo.5506946 2021-09-14T23:59:59 https://opensource.org/licenses/MIT 2022-07-15T11:28:00 Khaos Research Group (c) Khaos Research Group, University of Málaga SALON - Pairwise and Multiple Sequence ALignment ONtology SALON - Sequence ALingment Ontology for pairwise and multiple sequence alignments salon https://w3id.org/salon# SALON - Sequence ALingment Ontology for pairwise and multiple sequence alignments SALON - Pairwise and Multiple Sequence ALignment ONtology v1.0.2 Has Association With Has Construction Method Has Alignment Score Has Alignment Score Function Has Column Has Column Score Has Column Score Function Has Feature Has Sequence Has Subalignment Is Column Of Is Feature Of Is Sequence Of Is Subalignment Of Protein recommended name Mnemonic Feature note Feature score The start position of the feature. Feature start The end position of the feature. Feature stop Feature type A unique identifier in the databases. Accession numbers should remain static between database updates. Accession number The position of the column in the alignment. Sequence index Alignment column data (one character for each sequence). Column A weight associated with a given column. Column weight A consensus character that summarises the residue information contained in an alignment column. Consensus character A general description of the entity. Description The character used to represent an insertion/deletion. Gap character The gene by which the protein is encoded. Protein gene The name or UID given to the sequence. Sequence Identifier A keyword provides information that can be used to generate indexes of the entries based on functional, structural, or other categories. Keyword The length of the sequence. Sequence length The unique identifier of the organism that was the source of the sequence by the NCBI. Sequence organism Protein description Recommended name of the protein associated to the amino acid sequence. Protein name A score or metric computed for the alignment. Score Cutoff value is used as a classification criterion to separate columns into reliable and unreliable based on the score value. Score Cutoff Score Max Score Min The sequence itself, made up of residues and gap characters. Sequence SubAlignment name Set of biological sequences, used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between them. Alignment A representation of a column in the alignment. Note that a column with all gaps is not allowed. Alignment Column 1 A score given to the alignment. Alignment Score The method used to calculate the scoring function. Alignment Score Function An ordered succession of residues and gap characters in a sequence. For proteins, this is known as the primary structure. Alignment Sequence 1 A score given to a single column. Column Score The method used to calculate the scoring function for a given column. Column Score Function Column in the alignment with high confidence score. Confidently Aligned Column The method or algorithm used to construct the sequence alignment. Construction Method Valid alignment in terms of scoring. Correct Alignment Nucleotides Sequence. DNA Sequence Approach that produces the same alignment every time. Deterministic Approach Population-based optimization algorithm. Evolutionary algorithm Structural or functional feature associated with a sequence, e.g., a region of interest, a secondary structure element, etc. Feature Evolutionary computation technique inspired by biological evolution. Genetic Algorithm Probabilistic model that encapsulate the evolutionary changes of an alignment. Hidden Markov model Invalid alignment in terms of scoring. Incorrect Alignment Heuristic that realigns the sequences during multiple iterations of the alignment process. Iterative method The cost function to maximize (direction of optimization). Maximization Alignment Score Function The cost function to maximize (direction of optimization). Maximization Column Score Function The cost function to minimize (direction of optimization). Minimization Alignment Score Function The cost function to minimize (direction of optimization). Minimization Column Score Function The alignment starts with one sequence and progressively aligns the others. Progressive method The protein associated to an amino acid sequence. Protein Amino Acids Sequence. Protein Sequence Reliability measure to estimate alignment accuracy. Reliability Measure Approach that uses randomness to find an alignment. Stochastic Approach 2 A subset of sequences in the alignment. Sub Alignment Column in the alignment with low confidence score. Unconfidently Aligned Column 1.0 0.0 100 0 0.5 1.0 0.0 1.0 0.0 1 0 4.322 0.0 H ranges from 0 (only one residue in present at that position) to 4.322 (all 20 residues are equally represented in that position). Typically, positions with H >2.0 are considerered variable, whereas those with H < 2 are consider conserved. Highly conserved positions are those with H <1.0 (Litwin and Jores, 1992). A minimum number of sequences is however required (~100) for H to describe the diversity of a protein family. 1 0 Dynamic programming University of Málaga Antonio Benítez-Hidalgo University of Málaga Antonio Benítez-Hidalgo University of Málaga Antonio Benítez-Hidalgo University of Málaga Ismael Navas-Delgado University of Málaga Antonio Benítez-Hidalgo University of Málaga María del Mar Roldán-García University of Málaga María del Mar Roldán-García University of Málaga Antonio Benítez-Hidalgo University of Málaga Ismael Navas-Delgado University of Málaga Ismael Navas-Delgado University of Málaga Antonio Benítez Hidalgo University of Málaga María del Mar Roldán-García University of Málaga María del Mar Roldán-García University of Málaga Antonio Benítez-Hidalgo University of Málaga Ismael Navas-Delgado University of Málaga Ismael Navas-Delgado University of Málaga Ismael Navas-Delgado University of Málaga María del Mar Roldán-García University of Málaga María del Mar Roldán-García University of Málaga María del Mar Roldán-García University of Málaga María del Mar Roldán-García University of Málaga Antonio Benítez-Hidalgo University of Málaga Ismael Navas-Delgado University of Málaga Ismael Navas-Delgado University of Málaga Antonio Benítez-Hidalgo University of Málaga María del Mar Roldán-García University of Málaga Ismael Navas-Delgado University of Málaga Antonio Benítez-Hidalgo University of Málaga María del Mar Roldán-García University of Málaga Antonio Benítez-Hidalgo University of Málaga Antonio Benítez-Hidalgo University of Málaga Ismael Navas-Delgado University of Málaga Antonio Benítez-Hidalgo University of Málaga María del Mar Roldán-García University of Málaga Antonio Benítez-Hidalgo University of Málaga Ismael Navas-Delgado University of Málaga María del Mar Roldán-García University of Málaga Antonio Benítez-Hidalgo University of Málaga María del Mar Roldán-García University of Málaga Ismael Navas-Delgado University of Málaga Antonio Benítez-Hidalgo University of Málaga Antonio Benítez-Hidalgo University of Málaga María del Mar Roldán-García University of Málaga Ismael Navas-Delgado University of Málaga María del Mar Roldán-García University of Málaga Ismael Navas-Delgado University of Málaga María del Mar Roldán-García University of Málaga Ismael Navas-Delgado University of Málaga Ismael Navas-Delgado Thing true Confidently aligned column true Unconfidently aligned column true Alignment correctness true Alignment incorrectness