Protocols

OligoSpawn specifications

Information


Unique identifier OMICS_26489
Name OligoSpawn
Interface Web user interface
Restrictions to use None
Input format FASTA
Programming languages PHP
Computer skills Basic
Stability Stable
Source code URL http://www.oligospawn.org/dwn/oligospawn_src.zip
Registration required Yes
Maintained Yes

Maintainers


  • person_outline Stefano Lordi
  • person_outline Tao Jiang
  • person_outline Jie Zheng
  • person_outline Jan Svensson
  • person_outline Timothy Close

Information


Unique identifier OMICS_26489
Name OligoSpawn
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Programming languages C++, PHP
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Source code URL http://www.oligospawn.org/dwn/oligospawn_src.zip
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Stefano Lordi
  • person_outline Tao Jiang
  • person_outline Jie Zheng
  • person_outline Jan Svensson
  • person_outline Timothy Close

Publication for OligoSpawn

OligoSpawn citation

call_split

A compartmentalized approach to the assembly of physical maps

2009
BMC Bioinformatics
PMCID: 2717093
PMID: 19604400
DOI: 10.1186/1471-2105-10-217
call_split See protocol

[…] We used the genomic data of two plants, namely barley and rice, to compare our compartmentalized approach to the standard FPC assembly.For barley, we used OLIGOSPAWN[] to design 12,467 36-mer oligonucleotide probes from a dataset of 53,799 barley unigenes obtained from HarvEST website []. A unigene is obtained as a product of assembling several ESTs. Pr […]

OligoSpawn institution(s)
Department of Computer Science & Engineering, University of California, Riverside, CA, USA; Department of Botany & Plant Sciences, University of California, Riverside, CA, USA
OligoSpawn funding source(s)
Supported in part by NSF DBI-0321756, NSF CAREER IIS0447773, and USDA/CSREES 2001-52100-11346.

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