174,751 research outputs found
Type-IV DCT, DST, and MDCT algorithms with reduced numbers of arithmetic operations
We present algorithms for the type-IV discrete cosine transform (DCT-IV) and
discrete sine transform (DST-IV), as well as for the modified discrete cosine
transform (MDCT) and its inverse, that achieve a lower count of real
multiplications and additions than previously published algorithms, without
sacrificing numerical accuracy. Asymptotically, the operation count is reduced
from ~2NlogN to ~(17/9)NlogN for a power-of-two transform size N, and the exact
count is strictly lowered for all N > 4. These results are derived by
considering the DCT to be a special case of a DFT of length 8N, with certain
symmetries, and then pruning redundant operations from a recent improved fast
Fourier transform algorithm (based on a recursive rescaling of the
conjugate-pair split radix algorithm). The improved algorithms for DST-IV and
MDCT follow immediately from the improved count for the DCT-IV.Comment: 11 page
A methodology for determining amino-acid substitution matrices from set covers
We introduce a new methodology for the determination of amino-acid
substitution matrices for use in the alignment of proteins. The new methodology
is based on a pre-existing set cover on the set of residues and on the
undirected graph that describes residue exchangeability given the set cover.
For fixed functional forms indicating how to obtain edge weights from the set
cover and, after that, substitution-matrix elements from weighted distances on
the graph, the resulting substitution matrix can be checked for performance
against some known set of reference alignments and for given gap costs. Finding
the appropriate functional forms and gap costs can then be formulated as an
optimization problem that seeks to maximize the performance of the substitution
matrix on the reference alignment set. We give computational results on the
BAliBASE suite using a genetic algorithm for optimization. Our results indicate
that it is possible to obtain substitution matrices whose performance is either
comparable to or surpasses that of several others, depending on the particular
scenario under consideration
Linking de novo assembly results with long DNA reads by dnaasm-link application
Currently, third-generation sequencing techniques, which allow to obtain much
longer DNA reads compared to the next-generation sequencing technologies, are
becoming more and more popular. There are many possibilities to combine data
from next-generation and third-generation sequencing.
Herein, we present a new application called dnaasm-link for linking contigs,
a result of \textit{de novo} assembly of second-generation sequencing data,
with long DNA reads. Our tool includes an integrated module to fill gaps with a
suitable fragment of appropriate long DNA read, which improves the consistency
of the resulting DNA sequences. This feature is very important, in particular
for complex DNA regions, as presented in the paper. Finally, our implementation
outperforms other state-of-the-art tools in terms of speed and memory
requirements, which may enable the usage of the presented application for
organisms with a large genome, which is not possible in~existing applications.
The presented application has many advantages as (i) significant memory
optimization and reduction of computation time (ii) filling the gaps through
the appropriate fragment of a specified long DNA read (iii) reducing number of
spanned and unspanned gaps in the existing genome drafts.
The application is freely available to all users under GNU Library or Lesser
General Public License version 3.0 (LGPLv3). The demo application, docker image
and source code are available at http://dnaasm.sourceforge.net.Comment: 16 pages, 5 figure
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