Tag: Parse

pymzML 2.5.0 – Python module to Parse mzML data based on cElementTree

pymzML 2.5.0

:: DESCRIPTION

pymzML is an extension to Python that offers

  • easy access to mass spectrometry (MS) data that allows the rapid development of tools,
  • a very fast parser for mzML data, the standard in mass spectrometry data format
  • a set of functions to compare or handle spectra

::DEVELOPER

CELLULAR AND MOLECULAR FUNCTIONS OF REACTIVE OXYGEN SPECIES

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Python

:: DOWNLOAD

 pymzML

:: MORE INFORMATION

Citation

Bald, T., Barth, J., Niehues, A., Specht, M., Hippler, M., and Fufezan, C. (2012)
pymzML – Python module for high throughput bioinformatics on mass spectrometry data,
Bioinformatics, doi: 10.1093/bioinformatics/bts066

MMCIF Dictionary Suite 2.300 – Parse, Validate, Manage data dictionaries used by the PDB

MMCIF Dictionary Suite 2.300

:: DESCRIPTION

MMCIF Dictionary Suite is a collection of tools to parse, validate, manage data dictionaries used by the PDB. Applications are also included, which convert data dictionaries to XML schema, provide HTML browsing, produce mapping information for relational database loaders (Db Loader) and convert data files between related CIF dialects

::DEVELOPER

RCSB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   MMCIF Dictionary Suite

:: MORE INFORMATION

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

Validate Fasta File 2.2.7887 – Parse Fasta file and return the number of proteins and number of Residues

Validate Fasta File 2.2.7887

:: DESCRIPTION

The Validate Fasta File utility is a Windows command-line application that will parse a Fasta file and return the number of proteins and number of residues in the file. Additionally, it will check the validity of the fasta file looking for common, known problems.

::DEVELOPER

Biological MS Data and Software Distribution Center , Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Microsoft NET Framework 4.0

:: DOWNLOAD

 Validate Fasta File utility

:: MORE INFORMATION

AceParser 1.33 – Parse an Ace file (Phred/Phrap output) into a tab-delimited Assembly Alignment file

AceParser 1.33

:: DESCRIPTION

AceParser: Parse an Ace file (Phred/Phrap output) into a tab-delimited assembly alignment file. Options to include embedded annotation from multiple sources.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 AceParser

:: MORE INFORMATION

Uniprot DAT File Parser 1.1.5674 – Read Uniprot (IPI) .Dat file and Parse out the information for each entry

Uniprot DAT File Parser 1.1.5674

:: DESCRIPTION

The Uniprot DAT File Parser can read a Uniprot (IPI) .Dat file and parse out the information for each entry, creating a tab delimited text file. Uniprot .Dat files can be obtained from EBI’s FTP site.

::DEVELOPER

Biological MS Data and Software Distribution Center , Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Microsoft NET Framework 3.5

:: DOWNLOAD

 Uniprot DAT File Parser

:: MORE INFORMATION

MFPaQ 4.0.0 – Parse, Validate, and Quantify MS Proteomics Data

MFPaQ 4.0.0

:: DESCRIPTION

MFPaQ (Mascot File Parsing and Quantification ) is a new web application dedicated to parse, validate, and quantify proteomics data. It allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).

::DEVELOPER

the MFPaQ developper

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsx
  • Firefox 2 or higher
  • Mascot server 2.1 or higher
  • Apache
  • Perl

:: DOWNLOAD

 MFPaQ

:: MORE INFORMATION

Citation

Bouyssié D, Gonzalez de Peredo A, Mouton E, Albigot R, Roussel L, Ortega N, Cayrol C, Burlet-Schiltz O, Girard J-P, and Monsarrat B.
MFPaQ, a new software to parse, validate, and quantify proteomic data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomic study of membrane proteins from primary human endothelial cells
Molecular & Cellular Proteomics, 6, 1621-1637

EmblEx 20121203 – Parse and Extract data from EMBL entries to various formats

EmblEx 20121203

:: DESCRIPTION

EmblEx (EMBL Extractor) is a software for molecular biologists and bioinformaticians. It consists of a series of perl scripts and makes use of a MySQL database. Using EmblEx is through a graphical interface within a web browser or through the command line under linux or windows.

::DEVELOPER

Virtual Biology Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 EmblEx

:: MORE INFORMATION

LIS alignment – Parse BLAST output using the LIS (Longest Increasing Subsequence) algorithm

LIS alignment

:: DESCRIPTION

LIS alignment is a www interface for parsing BLAST output using the LIS (Longest Increasing Subsequence) algorithm. The softwar processes the BLAST result to find the longest consecutive list of HSPs.

::DEVELOPER

Hongyu Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No

:: MORE INFORMATION

Citation

Hongyu Zhang
Alignment of BLAST high-scoring segment pairs based on the longest increasing subsequence algorithm
BIOINFORMATICS Vol. 19 no. 11 2003, pages 1391–1396

MitoBank 2.1 – Automatic Retrieval and Parsing of Mitochondrial Genomes

MitoBank 2.1

:: DESCRIPTION

MitoBank is a simple perl script to obtain from GeneBank mitochondrial genomes, parse them, and store the different genes in separate files. It can be used to retrieve both coding genes and RNA genes. Coding genes might be obtained in their amino acid or nucleotide sequence.

::DEVELOPER

Phylogenomics Group at the University of Vigo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MitoBank

:: MORE INFORMATION

Citation:

Abascal F, Posada D, Zardoya R. (2007)
MtArt: A new model of amino acid replacement for Arthropoda.
Molecular Biology and Evolution 24: 1-5.

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