MusicBLAST - Gapped Sequence Alignment for MIR

نویسندگان

  • Jürgen Kilian
  • Holger H. Hoos
چکیده

We propose an algorithm, MusicBLAST, for approximate pattern search/matching on symbolic musical data. MusicBLAST is based on the BLAST algorithm, one of the most commonly used algorithms for similarity search on biological sequence data [1, 2]. MusicBLAST can be used in combination with an arbitrary similarity measure (e.g., melodic, rhythmic or combined) and retrieves multiple occurrences of a given search pattern and its variations. Different from many other pattern matching techniques, it can find incomplete and imperfect occurrences of a given pattern, and produces a significance measure for the accuracy and quality of its results. Like BLAST — and different from many musical pattern matching approaches — MusicBLAST retrieves heuristically optimised bi-directional alignments searching iteratively in forward and backward direction by starting at a dedicated seed note position of a performance.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

A direct method for computing extreme value (Gumbel) parameters for gapped biological sequence alignments

We develop a general method for computing extreme value distribution (Gumbel, 1958) parameters for gapped alignments. Our approach uses mixture distribution theory to obtain associated BLOSUM matrices for gapped alignments, which in turn are used for determining significance of gapped alignment scores for pairs of biological sequences. We compare our results with parameters already obtained in ...

متن کامل

Gapped Extension for Local Multiple Alignment of Interspersed DNA Repeats

The identification of homologous DNA is a fundamental building block of comparative genomic and molecular evolution studies. To date, pairwise local sequence alignment methods have been the prevailing technique to identify homologous nucleotides. However, existing methods that identify and align all homologous nucleotides in one or more genomes have suffered poor scalability and limited accurac...

متن کامل

Design and Implementation of an FPGA-based Core for Gapped BLAST Sequence Alignment with the Two-Hit Method

-This paper presents the design and implementation of the first FPGA-based core for Gapped BLAST sequence alignment with the two-hit method, ever reported in the literature. Gapped BLAST with two hit is a heuristic biological sequence alignment algorithm which is very widely used in the Bioinformatics and Computational Biology world. The architecture of the core is parameterized in terms of seq...

متن کامل

ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches

SUMMARY We have developed a tool, called ProbeMatch, for matching a large set of oligonucleotide sequences against a genome database using gapped alignments. Unlike most of the existing tools such as ELAND which only perform ungapped alignments allowing at most two mismatches, ProbeMatch generates both ungapped and gapped alignments allowing up to three errors including insertion, deletion and ...

متن کامل

SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments

MOTIVATION Optimal sequence alignment based on the Smith-Waterman algorithm is usually too computationally demanding to be practical for searching large sequence databases. Heuristic programs like FASTA and BLAST have been developed which run much faster, but at the expense of sensitivity. RESULTS In an effort to approximate the sensitivity of an optimal alignment algorithm, a new algorithm h...

متن کامل

ذخیره 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 نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2004