Sequence embedding for fast construction of guide trees for multiple sequence alignment 英文参考文献.docVIP

Blackshields et al. Algorithms for Molecular Biology 2010, 5:21 /content/5/1/21 RESEARCH Open Access Sequence embedding for fast construction of Research guide trees for multiple sequence alignment Gordon Blackshields, Fabian Sievers*, Weifeng Shi, Andreas Wilm and Desmond G Higgins Abstract 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 N2 for N sequences. When N grows larger than 10,000 or so, this becomes increasingly prohibitive and can form a significant barrier to carrying out very large multiple alignments. Results: In this paper, we have tested variations on a class of embedding methods that have been designed for clustering large numbers of complex objects where the individual distance calculations are expensive. These methods involve embedding the sequences in a space where the similarities within a set of sequences can be closely approximated without having to compute all pair-wise distances. Conclusions: We show how this approach greatly reduces computation time and memory requirements for clustering large numbers of sequences and demonstrate the quality of the clusterings by benchmarking them as guide trees for multiple alignment. Source code is available for download from /mbed.tgz. Introduction The majority of multiple sequence alignment (MSA) more important. For example, the Ribosomal Database align greater numbers of sequences is becoming even methods use some form of progressive alignment [1-7]. Project [10] Release 10 consists of more than a million In progressive alignment the usual first step is to compute a pair-wise distance matrix which is then used to make a sequences. In order to make very large guide trees, the first issue is so called guide tree, in order