subSeq statistics

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subSeq specifications

Information


Unique identifier OMICS_05533
Name subSeq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License MIT License
Computer skills Advanced
Version 1.4.1
Stability Stable
Maintained Yes

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Publication for subSeq

subSeq in pipelines

 (2)
2018
PMCID: 5879832
PMID: 29609542
DOI: 10.1186/s12866-018-1171-2

[…] phix sequences were removed by mapping the reads to the phix reference genome (genbank acc. nr. j02482.1) using “bwa mem” with default settings []. reads aligning were removed using seqtk with the subseq command []. downstream processing and sequence analysis was performed using mothur (v. 1.36.1) according to the mothur illumina miseq sop []. briefly, paired-end reads were joined using […]

2018
PMCID: 5918799
PMID: 29694397
DOI: 10.1371/journal.pone.0195481

[…] plastids hits are reported in , and tables., reads assigned to the species t. trichiura and t. muris and the ascaris genus by the lca algorithm, were extracted using seqtk version 1.0-r31 and the subseq command. reads were re-mapped to the t. trichiura sequence from humans in uganda (kt449826), the ascaris sp. sequence from haplotype 07 (pug3-1-h07) or the t. muris sequence (nc_028621) using […]


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subSeq in publications

 (6)
PMCID: 5918799
PMID: 29694397
DOI: 10.1371/journal.pone.0195481

[…] plastids hits are reported in , and tables., reads assigned to the species t. trichiura and t. muris and the ascaris genus by the lca algorithm, were extracted using seqtk version 1.0-r31 and the subseq command. reads were re-mapped to the t. trichiura sequence from humans in uganda (kt449826), the ascaris sp. sequence from haplotype 07 (pug3-1-h07) or the t. muris sequence (nc_028621) using […]

PMCID: 5879832
PMID: 29609542
DOI: 10.1186/s12866-018-1171-2

[…] phix sequences were removed by mapping the reads to the phix reference genome (genbank acc. nr. j02482.1) using “bwa mem” with default settings []. reads aligning were removed using seqtk with the subseq command []. downstream processing and sequence analysis was performed using mothur (v. 1.36.1) according to the mothur illumina miseq sop []. briefly, paired-end reads were joined using […]

PMCID: 3706340
PMID: 23902516
DOI: 10.1186/1471-2105-14-S5-S18

[…] between the lengths of the shorter and the longer repeats. the probability this pair is unbridged is (pℓinter1eavedunbridged)2, where, (3) p ℓ unbridged : = ℙ [ ℓ - length subseq . is unbridged ] = e n g ( l - ℓ - 1 ) + . , theorem 1 implies that the probability of making an error in the reconstruction […]

PMCID: 2701420
PMID: 19445721
DOI: 10.1186/1471-2105-10-150

[…] string of amino acid, ◦ e.g. a = {acd, efg, am}, concatenate(a) = acdefgam, • length: s → n, ◦ length(s) – returns the length of the sequence s, • addseq(e, a) – adds the element e to the set a, • subseq: s × n × n → s, ◦ subseq(s, d, n) – returns subsequence of s that starts at position d and has a window size n, ◦ e.g. subseq(abdefg, 2,3) = def, • merge(a, b) – merges two row-vectors […]

PMCID: 2490759
PMID: 18559360
DOI: 10.1093/nar/gkn358

[…] were picked at random and used to inoculate 5 ml of lb broth containing 15 μg/ml kan. plasmid dna was isolated from each culture using the qiaprep spin miniprep kit (qiagen ltd, crawley, uk). subseq was removed from the plasmid (ca 2 μg per 50 μl reaction volume) by digestion with mlyi. the plasmid (ca 20 ng) was recircularized directly after digestion using t4 dna ligase (promega uk, […]


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subSeq institution(s)
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Molecular Biology, Princeton University, Princeton, NJ, USA
subSeq funding source(s)
This work was supported by NIH (R01 HG002913).

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