Using multiple alignments to improve seeded local alignment algorithms
نویسندگان
چکیده
منابع مشابه
Using multiple alignments to improve seeded local alignment algorithms
Multiple alignments among genomes are becoming increasingly prevalent. This trend motivates the development of tools for efficient homology search between a query sequence and a database of multiple alignments. In this paper, we present an algorithm that uses the information implicit in a multiple alignment to dynamically build an index that is weighted most heavily towards the promising region...
متن کاملUsing Multiple Alignments to Improve Gene Prediction
The multiple species de novo gene prediction problem can be stated as follows: given an alignment of genomic sequences from two or more organisms, predict the location and structure of all protein-coding genes in one or more of the sequences. Here, we present a new system, N-SCAN (a.k.a. TWINSCAN 3.0), for addressing this problem. N-SCAN can model the phylogenetic relationships between the alig...
متن کاملMultiple alignment by aligning alignments
MOTIVATION Multiple sequence alignment is a fundamental task in bioinformatics. Current tools typically form an initial alignment by merging subalignments, and then polish this alignment by repeated splitting and merging of subalignments to obtain an improved final alignment. In general this form-and-polish strategy consists of several stages, and a profusion of methods have been tried at every...
متن کاملCombining Multiple Alignments to Improve Machine Translation
Word alignment is a critical component of machine translation systems. Various methods for word alignment have been proposed, and different models can produce significantly different outputs. To exploit the advantages of different models, we propose three ways to combine multiple alignments for machine translation: (1) alignment selection, a novel method to select an alignment with the least ex...
متن کاملStatistics of local multiple alignments
SUMMARY BLAST statistics have been shown to be extremely useful for searching for significant similarity hits, for amino acid and nucleotide sequences. Although these statistics are well understood for pairwise comparisons, there has been little success developing statistical scores for multiple alignments. In particular, there is no score for multiple alignment that is well founded and treated...
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: Nucleic Acids Research
سال: 2005
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gki767