Protocols

ProbeLynx specifications

Information


Unique identifier OMICS_24029
Name ProbeLynx
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Mammals
    • Bos taurus
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus

Maintainers


This tool is not available anymore.

Additional information


http://koch.pathogenomics.ca/probelynx/documentation.php

Information


Unique identifier OMICS_24029
Name ProbeLynx
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data An oligo array.
Input format FASTA,TSV
Output data A summary file and separate annotation files.
Output format TSV
Operating system Unix/Linux
Programming languages Perl
Database management system MySQL
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2.2
Stability Stable
Requirements
The Perl Config, BLAT
Maintained No

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Mammals
    • Bos taurus
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus

Download


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Versioning


No version available

Maintainers


This tool is not available anymore.

Additional information


http://koch.pathogenomics.ca/probelynx/documentation.php

Publication for ProbeLynx

ProbeLynx citations

 (2)
call_split

ApiAP2 Factors as Candidate Regulators of Stochastic Commitment to Merozoite Production in Theileria annulata

2015
PLoS Negl Trop Dis
PMCID: 4537280
PMID: 26273826
DOI: 10.1371/journal.pntd.0003933
call_split See protocol

[…] to match probe sequences to annotated spliced gene sequences. The sequence of each probe on the array was mapped to coding sequences utilising a flagging system similar to the web-based application, ProbeLynx []. A flag value of 1 represents a perfect, full-length alignment between a probe and gene, while a flag value of 5 represents poor alignment. For each individual probe, if a clear best matc […]

library_books

IMAD: flexible annotation of microarray sequences

2009
BMC Proc
PMCID: 2712745
PMID: 19615115
DOI: 10.1186/1753-6561-3-S4-S2

[…] om annotation based on incomplete genomes and incorrect or incomplete annotation. This may result in an incomplete coverage of the genome, non-specific probes, incorrect annotation, and orphan probes.ProbeLynx [] is a software system that has been published to accomplish the task of linking microarray sequences to annotation data. However, ProbeLynx uses certain tables directly from the Ensembl da […]

ProbeLynx institution(s)
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; VIDO, Saskatoon, SK, Canada; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
ProbeLynx funding source(s)
Supported by the Functional Pathogenomics of Mucosal Immunity (FPMI) Project of Genome Canada/Genome Prairie/Genome BC, with support from Inimex Pharmaceuticals Inc. (BC, Canada) and by a Canada Research Chair.

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