Sequence embedding for fast construction of guide trees for multiple sequence alignment
نویسندگان
چکیده
منابع مشابه
Sequence embedding for fast construction of guide trees
Background: The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences. This requires memory and time proportional to N for N sequences. When N grows larger than 10,000 or so, this becomes increasingly prohibitive and can form a signif...
متن کاملEvolving Guide Trees in Progressive Multiple Sequence Alignment
We present a novel application of genetic algorithms to the problem of aligning multiple biological sequences through the optimization of guide trees. Individual guide trees are represented as coalescing binary trees which provide for efficient and meaningful crossover and mutation operations. We hypothesize that our technique avoids the limitations of other heuristic tree-building techniques, ...
متن کاملFast A Algorithms for Multiple Sequence Alignment
The multiple alignment of the sequences of DNA and proteins is applicable to various important elds in molecular biology. Although the approach based on Dynamic Programming is well-known for this problem, it requires enormous time and space to obtain the optimal alignment. On the other hand, this problem corresponds to the shortest path problem and the A algorithm, which can e ciently nd the sh...
متن کاملMultiple Sequence Alignment Multiple Sequence Alignment
An algorithm for progressive multiple alignment of sequences with insertions " , 1. Introduction The problem of sequence alignment is to find the patterns of sequence conservation and similarity between pairs or sets of given sequences. In biological contexts, similarity between biological sequences usually amounts to either functional or structural similarities or divergence from a common ance...
متن کاملConstructing Phylogenetic Trees using Multiple Sequence Alignment
Constructing Phylogenetic Trees using Multiple Sequence Alignment Ryan M. Potter Chair of the Supervisory Committee: Professor Isabelle Bichindaritz Computing and Software Systems Phylogenetics is the study of evolutionary relatedness amongst organisms. The genetic relationships between species can be represented using phylogenetic trees. Advances in genomics have enriched the range of computat...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Algorithms for Molecular Biology
سال: 2010
ISSN: 1748-7188
DOI: 10.1186/1748-7188-5-21