MUSCLE: multiple sequence alignment with high accuracy and high throughput
نویسندگان
چکیده
منابع مشابه
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and C...
متن کاملMUSCLE: Low-complexity multiple sequence alignment with T-Coffee accuracy
MUSCLE ALGORITHM ABSTRACT We describe MUSCLE, a new program for creating multiple alignments of protein sequences. MUSCLE achieves the highest score so far reported on the BAliBASE benchmark, with average accuracy statistically indistinguishable from T-Coffee. MUSCLE aligns 5,000 sequences of average length 350 in 7 minutes on a current desktop computer, requiring less time than all other teste...
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Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under differ...
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Although genomewide association studies have successfully identified associations of many common single-nucleotide polymorphisms (SNPs) with common diseases, the SNPs implicated so far account for only a small proportion of the genetic variability of tested diseases. It has been suggested that common diseases may often be caused by rare alleles missed by genomewide association studies. To ident...
متن کاملSINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
MOTIVATION In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numb...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2004
ISSN: 1362-4962
DOI: 10.1093/nar/gkh340