SWAMP: Sliding Window Alignment Masker for PAML
نویسندگان
چکیده
منابع مشابه
SWAMP: Sliding Window Alignment Masker for PAML
With the greater availability of genetic data, large genome-wide scans for positive selection increasingly incorporate data from a range of sources. These data sets may be derived from different sequencing methods, each of which has potential sources of error. Sequencing errors, compounded by alignment errors, greatly increase the number of false positives in tests for adaptive evolution. Genom...
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MOTIVATION Matches to repetitive sequences are usually undesirable in the output of DNA database searches. Repetitive sequences need not be matched to a query, if they can be masked in the database. RepeatMasker/Maskeraid (RM), currently the most widely used software for DNA sequence masking, is slow and requires a library of repetitive template sequences, such as a manually curated RepBase lib...
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Existing digital logic simulators typically depend on a discrete-time model of circuit behaviour. Whilst this approach is sufficient in many cases for the validation of the behaviour of synchronous circuits, it is not good at identifying glitches that are narrower than the available time resolution. Moreover, it is not generally feasible to accommodate uncertainty in delay time in such a way as...
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Constrained coding is used widely in digital communication and storage systems. In this paper, we study a generalized sliding window constraint called the skip-sliding window. A skip-sliding window (SSW) code is defined in terms of the length L of a sliding window, skip length J , and cost constraint E in each sliding window. Each valid codeword of length L+kJ is determined by k+1 windows of le...
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Sorted Sliding Window Compression (SSWC) uses a new model (Sorted Sliding Window Model | SSWM) to encode strings e cient, which appear again while encoding a symbol sequence. The SSWM holds statistics of all strings up to certain length k in a sliding window of size n (the sliding window is de ned like in lz77). The compression program can use the SSWM to determine if the string of the next sym...
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ژورنال
عنوان ژورنال: Evolutionary Bioinformatics
سال: 2014
ISSN: 1176-9343,1176-9343
DOI: 10.4137/ebo.s18193