Bioinformatik - glosor

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• Sequence pattern / fingerprint Protein fingerprints are groups of conserved motifs which can be used as diagnostic signatures to identify and characterize collections of protein sequences.
• Sequence similarity Sequence Similarity Searching is a method of searching sequence databases by using alignment to a query sequence.
• Fasta format A heuristic sequence comparison algorithm, used to search sequence databases for optimal local allignments to a query.
• Raw score The score of an allignment, usually defined as the sum of substitution and gap scores.
• E-value Expectation value. The number of distinct allignments with score equivalent or better than the one of interest that are expected to occur in a database search purely by chance. The lower the E-value the more significant the score is.
• Local allignment The allignment of segments from two nucleic acid or protein sequences.
• Heuristic A "guess". A rough approximation is made by the program to increase speed potentially at the cost of the quality of the results. BLAST and FASTA use heuretics based on knowledge of how sequences evolve.
• Sequence profile A linear model representing characteristics of a sequence group, the simplest form of which is the tabulation of the frequency of amino acids/nucleotides in each position of the multiple sequence allignment. Also called position-specific scoring matrices. Profiles that do not allow insertions and deletions are called weight matrices.
• HMM Hidden Markov Model. The extension of a Markov model. A pattern recognition method that can be used to represent the allignment of multiple sequences or sequence segments by attempting to capture common patterns of residue conservation.
• Rooted phylogenic tree A phylogenic tree in which the last common ancestor of all genes, or organisms, displayed on the tree is specified by the initial bifurcation of the tree.
• Redundant genetic code Redundancy in the genetic code means that most amino acids are specified by more than one mRNA codon.
• Python list Can be used to store a number of items, like an integer, variable, string, or even other lists in each unit. Things can be stored and read, moved and removed from the list.
• Paralogs Homologous sequences that diverged by gene duplication.
• Sequence identity Refers to the occurrence of exactly the same nucleotide or amino acid in the same position in aligned sequences.
• Markov model (Markov chain) A statistical model for sequences in which the probability of each letter depends on the letters that precede it.
• Low complexity region A region of a nucleic acid or protein sequence with highly biased residue composition, or consisting of many short near-perfect repeats.
• Domain A portion of a protein that folds independently of the rest of the protein, or is at least assumed to do so.
• Bit score A scaled version of an alligment's raw score that accounts for the statistical properties of the scoring system used.
• Homologs Similar or identical sequences of DNA.
• NR database Non-redundant database of protein or DNA sequences available from the NCBI BLAST website.
• Orthologs Homologous sequences in different species that arose from a common ancestor gene during speciation. May or may not be responsible for a similar function.
• Unrooted phylogenic tree A phylogenic tree in which the last common ancestor of all genes, or organisms, on the tree is not specified.
• Dynamic processing/programming A type of algorithm widely used for constructing sequence allignments and for evaluating all possible candidate gene structures.
• ORF Open reading frame. The region of DNA that is transcribed by a ribosome.
• Substitution matrix The collection of all substitution scores
• Substitution score The score for alligning a particular pair of letters
• Gap score The score assigned to a gap, which is when several adjacent null characters in one sequence are alligned with adjacent letters in the other.

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