FastaFormat / FastQFormat / UnFastaFormat / UnFastQFormat – Conversion between Tab-delimited files and FASTA/ FastQ Format

FastaFormat / FastQFormat / UnFastaFormat / UnFastQFormat

:: DESCRIPTION

FastaFormat: Convert tab-delimited files into fasta format. Includes a quality score safe option (-q) for converting quality score files.

FastQFormat: Convert tab-delimited sequence and quality score files into fastQ format.

UnFastaFormat: Convert fasta files into tab-delimited format. Includes a quality score safe option (-q) for converting quality score files.

UnFastQFormat: Convert fastq files into tab-delimited format. Outputs sequences and quality scores into separate files. Edits sequence titles. Support for NCBI and Illumina formats.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX /  Linux
  • Perl

:: DOWNLOAD

 FastaFormat / FastQFormat / UnFastaFormat / UnFastQFormat

:: MORE INFORMATION

MoSeC 1.2 – Conversion of Dynamic Models of Complex Genetic Circuits into Nucleotide Sequences Ready for Synthesising

MoSeC 1.2

:: DESCRIPTION

MoSeC (Model to Sequence Converter) is a Java application for synthetic biology design that takes a model annotated with the DNA sequence information of genetic elements and converts it into a DNA sequence.

::DEVELOPER

Interdisciplinary Computing and Complex BioSystems (ICOS) research group

:: SCREENSHOTS

MoSeC

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 MoSeC

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 1;27(7):973-9. doi: 10.1093/bioinformatics/btr048. Epub 2011 Feb 4.
Model annotation for synthetic biology: automating model to nucleotide sequence conversion.
Misirli G, Hallinan JS, Yu T, Lawson JR, Wimalaratne SM, Cooling MT, Wipat A.

WormBase Converter – Conversion of any Gene ID into any other Gene ID

WormBase Converter

:: DESCRIPTION

The WormBase Converter is a tool for researchers who need to produce up-to-date lists of C. elegans genes, for example starting with a large list culled from the literature.

::DEVELOPER

the Ewbank lab

:: SCREENSHOTS

WBConverter

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Python

:: DOWNLOAD

 WormBase Converter

:: MORE INFORMATION

Citation:

PLoS One. 2011;6(5):e19055. doi: 10.1371/journal.pone.0019055. Epub 2011 May 13.
A comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in C. elegans.
Engelmann I1, Griffon A, Tichit L, Montañana-Sanchis F, Wang G, Reinke V, Waterston RH, Hillier LW, Ewbank JJ.

PklFileMerger – Conversion of single Q-TOF pkl-files into larger Mergefiles

PklFileMerger

:: DESCRIPTION

PklFileMerger is a simple GUI-based software for conversion of single Q-TOF pkl-files into larger mergefiles before database searching. It can also output a format that emulates ThermoFinnegan with elution time and scan number. This is mainly for working with MSQuant.

::DEVELOPER

The Proteomics Unit at the University of Bergen (PROBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  PklFileMerger

:: MORE INFORMATION

RNA2D3D 5.7.0 – Conversion of RNA 2D Structures to 3D and 3D Modeling

RNA2D3D 5.7.0

:: DESCRIPTION

RNA2D3D accepts the primary RNA sequence information and a secondary structure representation for the sequence, which may include pseudoknots (Martinez et al. 2008). It rapidly generates a first-pass, three-dimensional model from the secondary structure. Further refinements of the models are usually necessary, but in many cases the first pass model will give significant insights as to how to proceed. Because of its speed and because of the flexibility of its structure editing tools, RNA2D3D can be used to quickly explore alternative 3D conformations in an interactive fashion (Note that it is not a de novo 3D structure prediction program.).

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/SGI/Irix

:: DOWNLOAD

 RNA2D3D

:: MORE INFORMATION

Citation:

J Biomol Struct Dyn. 2008 Jun;25(6):669-83.
RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA.
Martinez HM, Maizel JV Jr, Shapiro BA.

ProCon 0.9.804 – PROteomics CONversion tool

ProCon 0.9.804

:: DESCRIPTION

ProCon is a conversion tool written in Java for conversion of proteomics identification data into standard formats mzIdentML and Pride XML.

::DEVELOPER

Medizinisches Proteom-Center, Medical Bioinformatics

:: SCREENSHOTS

ProCon

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 ProCon

:: MORE INFORMATION

Citation

ProCon – PROteomics CONversion tool.
Mayer G, Stephan C, Meyer HE, Kohl M, Marcus K, Eisenacher M.
J Proteomics. 2015 Nov 3;129:56-62. doi: 10.1016/j.jprot.2015.06.015.

BISQUE 1.0 – a human Genomic, Proteomic, and Transcriptomic Conversion tool

BISQUE 1.0

:: DESCRIPTION

BISQUE (The Biological Sequence Exchange) is a bioinformatics tool enabling locus and variant-specific conversion among human gene, transcript, and protein identifiers from several popular databases.

::DEVELOPER

Yu Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

  BISQUE

:: MORE INFORMATION

Citation

BISQUE: locus- and variant-specific conversion of genomic, transcriptomic, and proteomic database identifiers.
Meyer MJ, Geske P, Yu H.
Bioinformatics. 2016 Jan 23. pii: btw043.

UNICON – Cheminformatics File Conversion

UNICON

:: DESCRIPTION

UNICON is a command-line tool to cope with common cheminformatics tasks. The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, and PDB via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states and conformer ensembles.

::DEVELOPER

Computational Molecular Design

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

UNICON 

:: MORE INFORMATION

fconv 1.24 – File Conversion

fconv 1.24

:: DESCRIPTION

fconv is a commandline tool concerning manipulating, converting, and analyzing data from different file formats, such as pdb(qt)-, mol2-, dlg-, cif- and sdf-files.

::DEVELOPER

Group of Prof. Dr. G. Klebe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

fconv

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 1;27(7):1021-2. doi: 10.1093/bioinformatics/btr055. Epub 2011 Feb 18.
fconv: Format conversion, manipulation and feature computation of molecular data.
Neudert G, Klebe G.

PDBinout 1.0.2 – Processing and Conversion of various versions of PDB file format

PDBinout 1.0.2

:: DESCRIPTION

PDBinout is an open-source, Python-based tool for processing and conversion of various versions of PDB file format for biostructural applications.

::DEVELOPER

Tomasz Woźniak

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 PDBinout

 :: MORE INFORMATION

Citation:

Acta Biochim Pol. 2013;60(4):591-3. Epub 2013 Dec 17.
Personalization of structural PDB files.
Woźniak T, Adamiak RW.