• residue
  • Alignment sensitivity is measured by correctly comparing predicted alignments of residue pairs to the total number of possible alignable pairs. (wikipedia.org)
  • This is calculated with the fraction: (pairs correctly aligned)/(pairs structurally alignable) Alignment precision is measured by the correctness of aligned residue pairs. (wikipedia.org)
  • The probability of emitting a particular residue is determined largely by the frequency at which that residue has been observed in that column of the alignment, but also incorporates prior information on patterns of residues that tend to co-occur in the same columns of sequence alignments. (wikipedia.org)
  • Global alignments, which attempt to align every residue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size. (wikipedia.org)
  • gaps
  • Inferring homologous relationships involves calculating scores of aligned pairs minus penalties for gaps. (wikipedia.org)
  • Each curated CDD alignment records conserved features within the family members in terms of 'blocks', the regions where every sequence is aligned without the gaps. (pubmedcentralcanada.ca)
  • The approach can be complicated by the presence of alignment gaps (commonly called indels) that indicate a structural region present in the target but not in the template, and by structure gaps in the template that arise from poor resolution in the experimental procedure (usually X-ray crystallography) used to solve the structure. (wikipedia.org)
  • 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 the following example, one has a weight matrix of 3 different sequences, without gaps. (wikipedia.org)
  • widely
  • While being widely accepted, progressive alignment has its own pitfalls as the misalignment made at previous stages can not be corrected afterwards and can propagate into serious alignment errors. (pubmedcentralcanada.ca)
  • The most widely used approach to multiple sequence alignments uses a heuristic search known as progressive technique (also known as the hierarchical or tree method) developed by Paulien Hogeweg and Ben Hesper in 1984. (wikipedia.org)
  • displaystyle
  • Due to this we define log 10 ⁡ 0 := − 10 {\displaystyle \log _{10}0:=-10} and take the (base 10) logarithm: This is our new weight matrix (WM). (wikipedia.org)
  • To do this, one has to add the numbers found at the position x i {\displaystyle x_{i}} of the logarithmic WM. (wikipedia.org)
  • molecular
  • Each amino acid side group has a limited volume to occupy and a limited number of possible interactions with other nearby side chains, a situation that must be taken into account in molecular modeling and alignments. (wikipedia.org)
  • secondary structure
  • These alignments can also take into account patterns of predicted or known secondary structure elements and can be scored using various statistical models. (wikipedia.org)
  • The detailed alignment view permits a user to examine individual aligned residues, matches between predicted and known secondary structure elements and the ability to toggle information regarding patterns of sequence conservation and secondary structure confidence. (wikipedia.org)
  • The three final output nodes deliver a score for each secondary structure element for the central position of the window. (wikipedia.org)
  • search
  • Although there many different interpretations of the word "library" among software developers, ProgrammableWeb adheres to a specific definition so as to clearly distinguish libraries from SDKs and frameworks in a way that will facilitate clean search results. (programmableweb.com)