Tag: format

PDB2PQR 3.2.0 – Convert Protein files in PDB format to PQR format

PDB2PQR 3.2.0

:: DESCRIPTION

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format.

::DEVELOPER

PDB2PQR Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

PDB2PQR

:: MORE INFORMATION

Citation

Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA.
PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations.
Nucleic Acids Res, 35, W522-5, 2007.

SPNConverter 1.0 – Tool to Convert Graphs into GraphML Format

SPNConverter 1.0

:: DESCRIPTION

SPNConverter enables users to automatically convert networks for analysis with the SPN simulator from the standard systems biology markup language (SBML) to Graphml format.

::DEVELOPER

Group of Clinical Genomic Networks

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • CytoScape
:: DOWNLOAD

 SPNConverter

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Oct 1;29(19):2507-8. doi: 10.1093/bioinformatics/btt421. Epub 2013 Aug 1.
SPNConverter: a new link between static and dynamic complex network analysis.
Dent JE1, Yang X, Nardini C.

hgvs 1.5.1 – Tools to Parse, Format, and Map Biological Sequence Variants

hgvs 1.5.1

:: DESCRIPTION

hgvs is a Python package to parse, format, and manipulate biological sequence variants according to recommendations of the Human Genome Variation Society.

::DEVELOPER

hgvs team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 hgvs

 :: MORE INFORMATION

Citation

A Python Package for Parsing, Validating, Mapping, and Formatting Sequence Variants Using HGVS Nomenclature.
Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA.
Bioinformatics. 2014 Sep 30. pii: btu630

BIOM-FORMAT 2.1.10 – The Biological Observation Matrix format

BIOM-FORMAT 2.1.10

:: DESCRIPTION

The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome.

::DEVELOPER

BIOM-FORMAT Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BIOM-FORMAT

:: MORE INFORMATION

Citation

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome.
Daniel McDonald, Jose C. Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, and J. Gregory Caporaso.
GigaScience 2012, 1:7 doi:10.1186/2047-217X-1-7

KEGGtranslator 2.5 – Visualizing and Converting the KEGG PATHWAY database to various formats

KEGGtranslator 2.5

:: DESCRIPTION

KEGGtranslator is an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g., MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator converts KEGG files (KGML formatted XML-files) to SBML, BioPAX, SIF, SBGN, SBML-qual, GML, GraphML, JPG, GIF, LaTeX, etc.

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

KEGGtranslator

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java

:: DOWNLOAD

   KEGGtranslator

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Aug 15;27(16):2314-5. doi: 10.1093/bioinformatics/btr377. Epub 2011 Jun 23.
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.
Wrzodek C, Dräger A, Zell A.

seqmagick 0.8.4 – Convert Sequence Files between Formats

seqmagick 0.8.4

:: DESCRIPTION

seqmagick is a kickass little utility to expose the file format conversion in BioPython in a convenient way.

::DEVELOPER

Frederick (Erick) Matsen’s Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 seqmagick

:: MORE INFORMATION

Checker 4.4.6 – Checking Biotechnology Sequence Listings for Compliance with Format

Checker 4.4.6

:: DESCRIPTION

Checker is a Microsoft Windows-based software application for checking biotechnology Sequence Listings for compliance with 37 Code of Federal Regulations (CFR) 1.821 – 1.825 for both ‘old rules’ (October 1990) and ‘new rules’ (July 1998).

::DEVELOPER

The Patent Electronic Business Center

:: SCREENSHOTS

checker

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Checker

:: MORE INFORMATION

Bio-Formats 6.6.1 – Java Library for Reading & Writing Biology Image File Formats

Bio-Formats 6.6.1

:: DESCRIPTION

Bio-Formats is a standalone Java library for reading and writing life sciences image file formats. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats. See the table below for a complete list (click the headers to sort, and format names to see all information).

Bio-Formats’s primary purpose is to convert proprietary microscopy data into an open standard called the OME data model, particularly into the OME-TIFF file format.

::DEVELOPER

development teams at The Open Microscopy Environment,

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • java

:: DOWNLOAD

Bio-Formats

:: MORE INFORMATION

iConvert – Convert Genotype Allele Formats

iConvert

:: DESCRIPTION

The iConvert program allows to convert genotype allele formats (any format for any SNP chip contained in the SNPchiMp tool).

::DEVELOPER

iConvert team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  MacOsX / Linux
  • Python

:: DOWNLOAD

 iConvert

:: MORE INFORMATION

Citation

SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species.
Nicolazzi EL, Caprera A, Nazzicari N, Cozzi P, Strozzi F, Lawley C, Pirani A, Soans C, Brew F, Jorjani H, Evans G, Simpson B, Tosser-Klopp G, Brauning R, Williams JL, Stella A.
BMC Genomics. 2015 Apr 10;16(1):283.