Staden protocols

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Staden computational protocol

Staden specifications

Information


Unique identifier OMICS_00894
Name Staden
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License BSD 2-clause “Simplified” License
Computer skills Medium
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Staden_Package

Subtools


  • Gap4
  • spin

Versioning


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Maintainer


  • person_outline James Bonfield <>

Publications for Staden

Staden IN pipelines

 (18)
2018
PMCID: 5796565
PMID: 29435100
DOI: 10.1186/s40793-017-0306-7

[…] a total of 221,447,771 bases and represented 41.5-fold genome coverage. these reads were assembled in newbler 2.8 software (roche), and gaps were closed by local assembly of selected reads in staden software [29] into a single circular contig., the ncbi prokaryotic genome annotation pipeline [30] was used for automated genome annotation, and functional annotations were carried […]

2018
PMCID: 5802896
PMID: 29414990
DOI: 10.1371/journal.pone.0192301

[…] maximal identity values of the four ehv-8 strains in comparison with ehv-1 and ehv-9., an alignment containing the four irish ehv-8 genome sequences and that of ehv-8 strain wh was created by using gap4 [27], and used as the basis for comparison. multiple sequence alignments of the predicted amino acid sequences of individual ehv-8 genes and of related genomes (s1 table) were created by using […]

2017
PMCID: 5441151
PMID: 28380111
DOI: 10.1590/S1678-9946201759010

[…] in 10 µl of formamide, submitted to heat shock, and sequenced in an abi 3130 automated sequencer (applied biosystems)., sense and anti-sense strand sequences of the ndh4 gene were examined in the staden software package version 1.5 35 , which produced a consensus strand for each sample. the sequences were aligned using the clustal x program version 1.83 36 ., relationships between mtdna […]

2016
PMCID: 4777767
PMID: 26941156
DOI: 10.1128/genomeA.01718-15

[…] technologies, while five were sequenced by 454 only. mira assembler version 4.0 (4) was used to assemble the reads into contigs, which were then proofread and corrected in the program gap5 of the staden software package (5). the genomes were annotated using the ncbi prokaryotic genome annotation pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok)., these draft genomes can provide […]

2016
PMCID: 4860592
PMID: 27157299
DOI: 10.1038/srep25634

[…] (sangon biotech, shanghai, china), all pcr products were sequenced directly with the pcr primers and internal primers generated by primer walking., contiguous sequence fragments were assembled using staden package v1.7.048. protein coding genes (pcgs) and ribosomal rna (rrna) genes were identified based on homologous regions of other insects using the clustal x4950. transfer rnas (trna) […]

Staden institution(s)
Laboratory of Molecular Biology, Hills Road, CB, Cambridge, UK

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