Tag: Sequence Variant

QSVanalyser 20121206 – Quantitative Analysis of Sequence Variants

QSVanalyser 20121206

:: DESCRIPTION

QSVanalyser is a program that allows rapid, user-controlled, batchwise analysis of DNA sequence traces for estimation of the relative proportions of two sequence variants (Quantitative Sequence Variants, QSVs).

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

QSVanalyser

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 QSVanalyser

:: MORE INFORMATION

Citation

Carr IM, Robinson JI, Dimitriou R, Markham AF, Morgan AW, Bonthron DT.
Inferring relative proportions of DNA variants from sequencing electropherograms
Bioinformatics 2009 December 25:3244-3250

AgileFileViewer 20130503 – Reads Sequence Variant File and Displays Associated Information for each Variant.

AgileFileViewer 20130503

:: DESCRIPTION

AgileFileViewer annotators sequence variants identified by AgileAnnotator and optionally filtered by AgileKnownSNPFilter so they can be visual inspected.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

AgileFileViewer

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 AgileFileViewer

:: MORE INFORMATION

AgileGeneFilter 20120105 – Allows Sequence Variants to be Filtered

AgileGeneFilter 20120105

:: DESCRIPTION

AgileGeneFilter allows sequence variants exported from AgileVariantViewer or AgileAnnotator to be filtered, by first identifying the proteins that are affected by the sequence variants and then performing a textual data search on these proteins, using information downloaded from the UNI-Prot web page.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

AgileGeneFilter

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 AgileGeneFilter

:: MORE INFORMATION

AgileKnownSNPFilter 20120105 – Analyses Sequence Variants

AgileKnownSNPFilter 20120105

:: DESCRIPTION

AgileKnownSNPFilter analyses sequence variants exported by AgileAnnotator and identifies those that have previously been found by the 1000 Genomes Project.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

AgileKnownSNPFilter

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 AgileKnownSNPFilter

:: MORE INFORMATION

AgileVariantViewer 20120105 – Allows Sequence Variants to be interactively Displayed and Filtered

AgileVariantViewer 20120105

:: DESCRIPTION

AgileVariantViewer allows sequence variants to be interactively displayed and filtered.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

AgileVariantViewer

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 AgileVariantViewer

:: MORE INFORMATION

AgileAnnotator 20140613 – Identifying Sequence Variants in ordered SAM files

AgileAnnotator 20140613

:: DESCRIPTION

AgileAnnotator identifies sequence variants that repeatedly occur in reads that have previously been aligned to a reference sequence by an alignment program, such as BWA or Novoalign, and exported as SAM files.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

AgileAnnotator

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 AgileAnnotator

:: MORE INFORMATION

AgileVariantMapper 20160629 – Visualise Sequence Variant data from Whole Exome Data

AgileVariantMapper 20160629

:: DESCRIPTION

AgileVariantMapper visualises sequence variant data from whole exome data, so that it is possible to identify autozygous regions in consanguineous individuals.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

AgileVariantMapper

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 AgileVariantMapper

:: MORE INFORMATION

Citation

Carr IM, Bhaskar S, O’Sullivan J, Aldahmesh MA, Shamseldin HE, Markham AF, Bonthron DT, Black G, Alkuraya FS.
Autozygosity mapping with exome sequence data.
Hum Mutat. 2013 Jan;34(1):50-6. doi: 10.1002/humu.22220. Epub 2012 Oct 22. PMID: 23090942.

tmVar 2.0 – Text Mining approach for Extracting Sequence Variants in Biomedical Literature

tmVar 2.0

:: DESCRIPTION

tmVar is a text-mining approach based on conditional random field (CRF) for extracting a wide range of sequence variants in both protein and gene levels according to a standard sequence variants nomenclature developed by the human genome variation society (HGVS).

::DEVELOPER

Zhiyong Lu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 tmVar

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1433-9. doi: 10.1093/bioinformatics/btt156. Epub 2013 Apr 5.
tmVar: a text mining approach for extracting sequence variants in biomedical literature.
Wei CH, Harris BR, Kao HY, Lu Z.