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Spaced Words specifications

Information


Unique identifier OMICS_05427
Name Spaced Words
Alternative name spaced
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data DNA sequences, protein sequences
Input format FASTA
Output data Distance matrix
Output format PHYLIP
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_05427
Name Spaced Words
Alternative name spaced
Interface Web user interface
Restrictions to use None
Input data DNA sequences, protein sequences
Input format FASTA
Output data Distance matrix
Output format PHYLIP
Computer skills Basic
Stability Stable
Source code URL http://spaced.gobics.de/content/spaced.tar.gz
Maintained Yes

Publications for Spaced Words

Spaced Words in publications

 (5)
PMCID: 5934817
PMID: 29724166
DOI: 10.1186/s12859-018-2148-8

[…] cartesian protein maps (nandy’s dna representation extended to proteins) [].k-mers or k-words: frequency of each subsequence or word of a fixed length k in a set of sequences [].spaced k-mers or spaced words: contiguous k-mers with “don’t care characters” at fixed or pre-defined positions in a set of sequences [].amino acid composition: the fraction of each amino acid within a protein [, […]

PMCID: 4918981
PMID: 27336403
DOI: 10.1371/journal.pcbi.1004985

[…] in that it runs on raw next-generation sequencing data. swf is similar to co-phylog, using a mask consisting of positions that are either match or don’t care, and using the frequencies of these spaced words, with the don’t care positions ignored according to the specified pattern., match length methods can also be divided into those allowing zero mismatches or those allowing some number […]

PMCID: 4194349
PMID: 24841985
DOI: 10.1016/j.cortex.2014.03.010

[…] found to disrupt reading in a patient with occipitoparietal lesions (). the current investigation found that pca patients with poor visuospatial processing were particularly inaccurate when reading spaced words. if reading spaced words demands support from dorsally-mediated reading strategies and/or involves greater visuospatial demands, the vulnerability of dorsal systems in pca (e.g., ) might […]

PMCID: 4007079
PMID: 24785494
DOI: 10.1038/srep04869

[…] this hyper-learned format, reading speed decreases and word length effects emerge, indicating a shift from parallel to effortful serial processing. this occurs with low-contrast, rotated, or highly spaced words as well as with words presented in case-alternation, zigzag or vertical mode. results of neuroimaging, erp and meg studies indicate that reading degraded words activates dorsal posterior […]

PMCID: 2248561
PMID: 18215291
DOI: 10.1186/1471-2105-9-37

[…] background models have been tested in this study. a first possibility is to estimate the prior probability of each dyad as the product of the frequencies observed in the input sequences for its two spaced words (monads)., p(w1nxw2) = f(w1)*f(w2). , where w1 and w2 are the two monads (in our case, trinucleotides) forming the dyad, nx represents the spacing of length x […]


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Spaced Words institution(s)
University of Göttingen, Department of Bioinformatics, Göttingen, Germany

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