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PMID- 16403221
OWN - NLM
STAT- MEDLINE
DA - 20060220
DCOM- 20060314
PUBM- Electronic
IS - 1471-2105 (Electronic)
VI - 7
DP - 2006
TI - A high level interface to SCOP and ASTRAL implemented in python.
PG - 10
AB - BACKGROUND: Benchmarking algorithms in structural bioinformatics often involves
the construction of datasets of proteins with given sequence and structural
properties. The SCOP database is a manually curated structural classification
which groups together proteins on the basis of structural similarity. The ASTRAL
compendium provides non redundant subsets of SCOP domains on the basis of
sequence similarity such that no two domains in a given subset share more than a
defined degree of sequence similarity. Taken together these two resources provide
a 'ground truth' for assessing structural bioinformatics algorithms. We present a
small and easy to use API written in python to enable construction of datasets
from these resources. RESULTS: We have designed a set of python modules to
provide an abstraction of the SCOP and ASTRAL databases. The modules are designed
to work as part of the Biopython distribution. Python users can now manipulate
and use the SCOP hierarchy from within python programs, and use ASTRAL to return
sequences of domains in SCOP, as well as clustered representations of SCOP from
ASTRAL. CONCLUSION: The modules make the analysis and generation of datasets for
use in structural genomics easier and more principled.
AD - Bioinformatics, Institute of Cell and Molecular Science, School of Medicine and
Dentistry, Queen Mary, University of London, London EC1 6BQ, UK.
j.a.casbon@qmul.ac.uk
FAU - Casbon, James A
AU - Casbon JA
FAU - Crooks, Gavin E
AU - Crooks GE
FAU - Saqi, Mansoor A S
AU - Saqi MA
LA - eng
PT - Evaluation Studies
PT - Journal Article
DEP - 20060110
PL - England
TA - BMC Bioinformatics
JT - BMC bioinformatics
JID - 100965194
SB - IM
MH - *Database Management Systems
MH - *Databases, Protein
MH - Information Storage and Retrieval/*methods
MH - Programming Languages
MH - Sequence Alignment/*methods
MH - Sequence Analysis, Protein/*methods
MH - Sequence Homology, Amino Acid
MH - *Software
MH - *User-Computer Interface
PMC - PMC1373603
EDAT- 2006/01/13 09:00
MHDA- 2006/03/15 09:00
PHST- 2005/06/17 [received]
PHST- 2006/01/10 [accepted]
PHST- 2006/01/10 [aheadofprint]
AID - 1471-2105-7-10 [pii]
AID - 10.1186/1471-2105-7-10 [doi]
PST - epublish
SO - BMC Bioinformatics. 2006 Jan 10;7:10.
PMID- 16377612
OWN - NLM
STAT- MEDLINE
DA - 20060223
DCOM- 20060418
LR - 20061115
PUBM- Print-Electronic
IS - 1367-4803 (Print)
VI - 22
IP - 5
DP - 2006 Mar 1
TI - GenomeDiagram: a python package for the visualization of large-scale genomic
data.
PG - 616-7
AB - SUMMARY: We present GenomeDiagram, a flexible, open-source Python module for the
visualization of large-scale genomic, comparative genomic and other data with
reference to a single chromosome or other biological sequence. GenomeDiagram may
be used to generate publication-quality vector graphics, rastered images and
in-line streamed graphics for webpages. The package integrates with datatypes
from the BioPython project, and is available for Windows, Linux and Mac OS X
systems. AVAILABILITY: GenomeDiagram is freely available as source code (under
GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires
Python 2.3 or higher, and recent versions of the ReportLab and BioPython
packages. SUPPLEMENTARY INFORMATION: A user manual, example code and images are
available at http://bioinf.scri.ac.uk/lp/programs.html.
AD - Plant Pathogen Programme, Scottish Crop Research Institute, Invergowrie, Dundee
DD2 5DA, Scotland, UK. lpritc@scri.ac.uk
FAU - Pritchard, Leighton
AU - Pritchard L
FAU - White, Jennifer A
AU - White JA
FAU - Birch, Paul R J
AU - Birch PR
FAU - Toth, Ian K
AU - Toth IK
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
DEP - 20051223
PL - England
TA - Bioinformatics
JT - Bioinformatics (Oxford, England)
JID - 9808944
SB - IM
MH - Chromosome Mapping/*methods
MH - *Computer Graphics
MH - *Database Management Systems
MH - *Databases, Genetic
MH - Information Storage and Retrieval/methods
MH - *Programming Languages
MH - *Software
MH - *User-Computer Interface
EDAT- 2005/12/27 09:00
MHDA- 2006/04/19 09:00
PHST- 2005/12/23 [aheadofprint]
AID - btk021 [pii]
AID - 10.1093/bioinformatics/btk021 [doi]
PST - ppublish
SO - Bioinformatics. 2006 Mar 1;22(5):616-7. Epub 2005 Dec 23.
PMID- 14871861
OWN - NLM
STAT- MEDLINE
DA - 20040611
DCOM- 20050104
LR - 20061115
PUBM- Print-Electronic
IS - 1367-4803 (Print)
VI - 20
IP - 9
DP - 2004 Jun 12
TI - Open source clustering software.
PG - 1453-4
AB - SUMMARY: We have implemented k-means clustering, hierarchical clustering and
self-organizing maps in a single multipurpose open-source library of C routines,
callable from other C and C++ programs. Using this library, we have created an
improved version of Michael Eisen's well-known Cluster program for Windows, Mac
OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to
the C Clustering Library, thereby combining the flexibility of a scripting
language with the speed of C. AVAILABILITY: The C Clustering Library and the
corresponding Python C extension module Pycluster were released under the Python
License, while the Perl module Algorithm::Cluster was released under the Artistic
License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well
as the corresponding command-line program, were released under the same license
as the original Cluster code. The complete source code is available at
http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively,
Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available
as part of the Biopython distribution.
AD - Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1
Shirokanedai, Minato-ku, Tokyo, 108-8639 Japan. mdehoon@ims.u-tokyo.ac.jp
FAU - de Hoon, M J L
AU - de Hoon MJ
FAU - Imoto, S
AU - Imoto S
FAU - Nolan, J
AU - Nolan J
FAU - Miyano, S
AU - Miyano S
LA - eng
PT - Comparative Study
PT - Evaluation Studies
PT - Journal Article
PT - Validation Studies
DEP - 20040210
PL - England
TA - Bioinformatics
JT - Bioinformatics (Oxford, England)
JID - 9808944
SB - IM
MH - *Algorithms
MH - *Cluster Analysis
MH - Gene Expression Profiling/*methods
MH - Pattern Recognition, Automated/methods
MH - *Programming Languages
MH - Sequence Alignment/*methods
MH - Sequence Analysis, DNA/*methods
MH - *Software
EDAT- 2004/02/12 05:00
MHDA- 2005/01/05 09:00
PHST- 2004/02/10 [aheadofprint]
AID - 10.1093/bioinformatics/bth078 [doi]
AID - bth078 [pii]
PST - ppublish
SO - Bioinformatics. 2004 Jun 12;20(9):1453-4. Epub 2004 Feb 10.
PMID- 14630660
OWN - NLM
STAT- MEDLINE
DA - 20031121
DCOM- 20040722
LR - 20061115
PUBM- Print
IS - 1367-4803 (Print)
VI - 19
IP - 17
DP - 2003 Nov 22
TI - PDB file parser and structure class implemented in Python.
PG - 2308-10
AB - The biopython project provides a set of bioinformatics tools implemented in
Python. Recently, biopython was extended with a set of modules that deal with
macromolecular structure. Biopython now contains a parser for PDB files that
makes the atomic information available in an easy-to-use but powerful data
structure. The parser and data structure deal with features that are often left
out or handled inadequately by other packages, e.g. atom and residue disorder (if
point mutants are present in the crystal), anisotropic B factors, multiple models
and insertion codes. In addition, the parser performs some sanity checking to
detect obvious errors. AVAILABILITY: The Biopython distribution (including source
code and documentation) is freely available (under the Biopython license) from
http://www.biopython.org
AD - Department of Cellular and Molecular Interactions, Vlaams Interuniversitair
Instituut voor Biotechnologie and Computational Modeling Lab, Department of
Computer Science, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels,
Belgium. thamelry@vub.ac.be
FAU - Hamelryck, Thomas
AU - Hamelryck T
FAU - Manderick, Bernard
AU - Manderick B
LA - eng
PT - Comparative Study
PT - Evaluation Studies
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
PT - Validation Studies
PL - England
TA - Bioinformatics
JT - Bioinformatics (Oxford, England)
JID - 9808944
RN - 0 (Macromolecular Substances)
SB - IM
MH - Computer Simulation
MH - Database Management Systems/*standards
MH - *Databases, Protein
MH - Information Storage and Retrieval/*methods/*standards
MH - Macromolecular Substances
MH - *Models, Molecular
MH - *Programming Languages
MH - Protein Conformation
MH - *Software
EDAT- 2003/11/25 05:00
MHDA- 2004/07/23 05:00
PST - ppublish
SO - Bioinformatics. 2003 Nov 22;19(17):2308-10.
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