SpEED: fast computation of sensitive spaced seeds
نویسندگان
چکیده
SUMMARY Multiple spaced seeds represent the current state-of-the-art for similarity search in bioinformatics, with applications in various areas such as sequence alignment, read mapping, oligonucleotide design, etc. We present SpEED, a software program that computes highly sensitive multiple spaced seeds. SpEED can be several orders of magnitude faster and computes better seeds than the existing leading software programs. AVAILABILITY The source code of SpEED is freely available at www.csd.uwo.ca/~ilie/SpEED/ CONTACT: [email protected] SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
منابع مشابه
Fast Computation of Good Multiple Spaced Seeds
Homology search finds similar segments between two biological sequences, such as DNA or protein sequences. A significant fraction of computing power in the world is dedicated to performing such tasks. The introduction of optimal spaced seeds by Ma et al. has increased both the sensitivity and the speed of homology search and it has been adopted by many alignment programs such as BLAST. With the...
متن کاملgpALIGNER: A Fast Algorithm for Global Pairwise Alignment of DNA Sequences
Bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity. Many computational algorithms have been applied for solving the sequence alignment problem. Dynamic programming, statistical methods, approximation and heuristic algorithms are the most common methods appli...
متن کاملComputing Alignment Seed Sensitivity with Probabilistic Arithmetic Automata
Heuristic sequence alignment and database search algorithms, such as PatternHunter and BLAST, are based on the initial discovery of so-called alignment seeds of well-conserved alignment patterns, which are subsequently extended to full local alignments. In recent years, the theory of classical seeds (matching contiguous q-grams) has been extended to spaced seeds, which allow mismatches within a...
متن کاملFast computation of neighbor seeds
MOTIVATION Alignment of biological sequences is one of the most frequently performed computer tasks. The current state of the art involves the use of (multiple) spaced seeds for producing high quality alignments. A particular important class is that of neighbor seeds which combine high sensitivity with reduced space requirements. Current algorithms for computing good neighbor seeds are very slo...
متن کاملSeed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping
Spaced seeds have been shown to be superior to continuous seeds for efficient and sensitive homology search based on the seedand-extend paradigm. Much the same is true in genome mapping of high-throughput short-read data. However, a highly sensitive search with multiple spaced patterns often requires the use of a great amount of index data. We propose a novel seed-set construction method for ef...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Bioinformatics
دوره 27 17 شماره
صفحات -
تاریخ انتشار 2011