Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points
نویسندگان
چکیده
منابع مشابه
Anchor points for genome alignment based on Filtered Spaced Word Matches
Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as anchor points to reduce the search space of the alignment procedure. Speed and quality of these methods therefore depend on the underlying anchor points. Herein, we propose to use Filtered Spaced Word Matches to calculate anchor poi...
متن کاملFast and accurate phylogeny reconstruction using filtered spaced-word matches
Motivation Word-based or 'alignment-free' algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. Results We propose Filtered Spaced Word Matches (FSWM) , a fast alignment-free...
متن کاملMultiple sequence alignment using anchor points through generalized dynamic programming
A generalization of the dynamic programming algorithm applied to the multiple alignment of protein sequences is proposed. The algorithm has two main procedures: (i) local correspondences between sequences hereafter called anchor points are selected according to a criterion that combines local and global simlilarity values, (ii) the alignment is constructed recursively by choosing and linking to...
متن کاملMultiple Genome Alignment by Clustering Pairwise Matches
We have developed a multiple genome alignment algorithm by using a sequence clustering algorithm to combine local pairwise genome sequence matches produced by pairwise genome alignments, e.g, BLASTZ. Sequence clustering algorithms often generate clusters of sequences such that there exists a common shared region among all sequences in each cluster. To use a sequence clustering algorithm for gen...
متن کاملINTERALIGN: interactive alignment editor for distantly related protein sequences
SUMMARY Improving and ascertaining the quality of a multiple sequence alignment is a very challenging step in protein sequence analysis. This is particularly the case when dealing with sequences in the 'twilight zone', i.e. sharing < 30% identity. Here we describe INTERALIGN, a dedicated user-friendly alignment editor including a view of secondary structures and a synchronized display of carbon...
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: Bioinformatics
سال: 2018
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bty592