PyCogent

A toolkit for making sense from sequence

Rob Knight, Peter Maxwell, Amanda Birmingham, Jason Carnes, James G Caporaso, Brett C. Easton, Michael Eaton, Micah Hamady, Helen Lindsay, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Michael Robeson, Raymond Sammut, Sandra Smit, Matthew J. Wakefield, Jeremy Widmann, Shandy Wikman, Stephanie Wilson, Hua Ying & 1 others Gavin A. Huttley

Research output: Contribution to journalArticle

128 Citations (Scopus)

Abstract

We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for third-party applications. The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from http://sourceforge.net/projects/pycogent.

Original languageEnglish (US)
Article numberR171
JournalGenome Biology
Volume8
Issue number8
DOIs
StatePublished - Aug 21 2007
Externally publishedYes

Fingerprint

Boidae
Python
Workflow
controllers
Licensure
hardware
Sequence Analysis
Publications
genomics
Databases
methodology
public
project

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Knight, R., Maxwell, P., Birmingham, A., Carnes, J., Caporaso, J. G., Easton, B. C., ... Huttley, G. A. (2007). PyCogent: A toolkit for making sense from sequence. Genome Biology, 8(8), [R171]. https://doi.org/10.1186/gb-2007-8-8-r171

PyCogent : A toolkit for making sense from sequence. / Knight, Rob; Maxwell, Peter; Birmingham, Amanda; Carnes, Jason; Caporaso, James G; Easton, Brett C.; Eaton, Michael; Hamady, Micah; Lindsay, Helen; Liu, Zongzhi; Lozupone, Catherine; McDonald, Daniel; Robeson, Michael; Sammut, Raymond; Smit, Sandra; Wakefield, Matthew J.; Widmann, Jeremy; Wikman, Shandy; Wilson, Stephanie; Ying, Hua; Huttley, Gavin A.

In: Genome Biology, Vol. 8, No. 8, R171, 21.08.2007.

Research output: Contribution to journalArticle

Knight, R, Maxwell, P, Birmingham, A, Carnes, J, Caporaso, JG, Easton, BC, Eaton, M, Hamady, M, Lindsay, H, Liu, Z, Lozupone, C, McDonald, D, Robeson, M, Sammut, R, Smit, S, Wakefield, MJ, Widmann, J, Wikman, S, Wilson, S, Ying, H & Huttley, GA 2007, 'PyCogent: A toolkit for making sense from sequence', Genome Biology, vol. 8, no. 8, R171. https://doi.org/10.1186/gb-2007-8-8-r171
Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC et al. PyCogent: A toolkit for making sense from sequence. Genome Biology. 2007 Aug 21;8(8). R171. https://doi.org/10.1186/gb-2007-8-8-r171
Knight, Rob ; Maxwell, Peter ; Birmingham, Amanda ; Carnes, Jason ; Caporaso, James G ; Easton, Brett C. ; Eaton, Michael ; Hamady, Micah ; Lindsay, Helen ; Liu, Zongzhi ; Lozupone, Catherine ; McDonald, Daniel ; Robeson, Michael ; Sammut, Raymond ; Smit, Sandra ; Wakefield, Matthew J. ; Widmann, Jeremy ; Wikman, Shandy ; Wilson, Stephanie ; Ying, Hua ; Huttley, Gavin A. / PyCogent : A toolkit for making sense from sequence. In: Genome Biology. 2007 ; Vol. 8, No. 8.
@article{bab22850d7ac4c51bd71844ac609c593,
title = "PyCogent: A toolkit for making sense from sequence",
abstract = "We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for third-party applications. The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from http://sourceforge.net/projects/pycogent.",
author = "Rob Knight and Peter Maxwell and Amanda Birmingham and Jason Carnes and Caporaso, {James G} and Easton, {Brett C.} and Michael Eaton and Micah Hamady and Helen Lindsay and Zongzhi Liu and Catherine Lozupone and Daniel McDonald and Michael Robeson and Raymond Sammut and Sandra Smit and Wakefield, {Matthew J.} and Jeremy Widmann and Shandy Wikman and Stephanie Wilson and Hua Ying and Huttley, {Gavin A.}",
year = "2007",
month = "8",
day = "21",
doi = "10.1186/gb-2007-8-8-r171",
language = "English (US)",
volume = "8",
journal = "Genome Biology",
issn = "1474-7596",
publisher = "BioMed Central",
number = "8",

}

TY - JOUR

T1 - PyCogent

T2 - A toolkit for making sense from sequence

AU - Knight, Rob

AU - Maxwell, Peter

AU - Birmingham, Amanda

AU - Carnes, Jason

AU - Caporaso, James G

AU - Easton, Brett C.

AU - Eaton, Michael

AU - Hamady, Micah

AU - Lindsay, Helen

AU - Liu, Zongzhi

AU - Lozupone, Catherine

AU - McDonald, Daniel

AU - Robeson, Michael

AU - Sammut, Raymond

AU - Smit, Sandra

AU - Wakefield, Matthew J.

AU - Widmann, Jeremy

AU - Wikman, Shandy

AU - Wilson, Stephanie

AU - Ying, Hua

AU - Huttley, Gavin A.

PY - 2007/8/21

Y1 - 2007/8/21

N2 - We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for third-party applications. The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from http://sourceforge.net/projects/pycogent.

AB - We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for third-party applications. The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from http://sourceforge.net/projects/pycogent.

UR - http://www.scopus.com/inward/record.url?scp=34748893838&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34748893838&partnerID=8YFLogxK

U2 - 10.1186/gb-2007-8-8-r171

DO - 10.1186/gb-2007-8-8-r171

M3 - Article

VL - 8

JO - Genome Biology

JF - Genome Biology

SN - 1474-7596

IS - 8

M1 - R171

ER -