• 2000
  • Birney is one of the founders of the Ensembl genome browser and other databases, and has played a key role in many large-scale genomics projects, notably the sequencing of the Human Genome in 2000 and the analysis of genome function in the ENCODE project. (wikipedia.org)
  • biologically relevant
  • RAMICS is a method developed at SANBI that undertakes fast and highly accurate mapping/alignment of coding sequence reads in a biologically relevant manner. (sanbi.ac.za)
  • RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. (sanbi.ac.za)
  • substitution
  • The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids whose side chains have similar biochemical properties) in a particular region of the sequence, suggest that this region has structural or functional importance. (wikipedia.org)
  • For nucleotide sequences a similar gap penalty is used, but a much simpler substitution matrix, wherein only identical matches and mismatches are considered, is typical. (wikipedia.org)
  • The scores in the substitution matrix may be either all positive or a mix of positive and negative in the case of a global alignment, but must be both positive and negative, in the case of a local alignment. (wikipedia.org)
  • inference
  • We take profit from some results on Grammatical Inference that allow us to build iteratively an abstract machine that considers in each inference step an increasing amount of sequences. (springer.com)
  • gene
  • Expressed Sequence Tag mapping of TMEM229B gene expression indicates that it is ubiquitously expressed throughout the body. (wikipedia.org)
  • local
  • one for finding complete matches to the HMM in longer sequences (say, if you're trying to find several complete copies of immunoglobulin domains in a neural cell adhesion molecule sequence), and one for finding multiple non-overlapping Smith/Waterman local alignments. (bio.net)
  • Use the MaxSegs/Waterman-Eggert version of the dynamic programming algorithm to provide the best local alignment and also to search for repeats. (bioinformatics.org)
  • common ancestor
  • If two sequences in an alignment share a common ancestor, mismatches can be interpreted as point mutations and gaps as indels (that is, insertion or deletion mutations) introduced in one or both lineages in the time since they diverged from one another. (wikipedia.org)
  • In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. (wikipedia.org)