Tag: Variant

RAREVATOR – RAre REference VAriant annotaTOR

RAREVATOR

:: DESCRIPTION

RAREVATOR is a tool for the identification and annotation of germline and somatic variants in rare reference allele loci from second generation sequencing data.

::DEVELOPER

RAREVATOR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RAREVATOR

:: MORE INFORMATION

Citation:

Characterization and identification of hidden rare variants in the human genome
Magi A, D’Aurizio R, Palombo F, Cifola I, Tattini L, Semeraro R, Pippucci T, Giusti B, Romeo G, Abbate R, Gensini GF.
BMC Genomics. 2015 Apr 24;16(1):340.

SPANR – Splicing-based Analysis of Variants

SPANR

:: DESCRIPTION

SPANR addresses a key unmet challenge in genomics research, which is to ascertain how single nucleotide variations (SNVs) cause splicing misregulation and may lead to disease. Unlike any other approach, this tool can analyze synonymous, missense and nonsense exonic SNVs, as well as intronic SNVs that are up to 300nt from splice junctions.

::DEVELOPER

the Frey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Hui Y. Xiong, et.al.
The human splicing code reveals new insights into the genetic determinants of disease.
Science DOI: 10.1126/science.1254806. Published Online December 18 2014.

PaPI – Pseudo Amino Acid Composition to Score human Protein-coding Variants

PaPI

:: DESCRIPTION

PaPI is a new machine-learning approach to classify and score human coding variants by estimating the probability to damage their protein-related function.

::DEVELOPER

laboratorio di Bioinformatica e Biologia Sintetica – Univ. of Pavia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PaPI: pseudo amino acid composition to score human protein-coding variants.
Limongelli I, Marini S, Bellazzi R.
BMC Bioinformatics. 2015 Apr 19;16(1):123. doi: 10.1186/s12859-015-0554-8.

SNVMix2 – Detect Single Nucleotide Variants from Next Generation Sequencing

SNVMix2

:: DESCRIPTION

SNVMix is designed to detect single nucleotide variants from next generation sequencing data. SNVMix is a post-alignment tool. Given a pileup file (either Maq or Samtools format) as input and model parameters, SNVMix will output the probability that each position is one of three genotypes:  aa (homozygous for the reference allele, where the reference is the genome the reads were aligned to), ab (heterozygous) and bb (homozygous for a non-reference allele).  A tool for fitting the model using expectation maximization is also supplied (use -T option).

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SNVMix

:: MORE INFORMATION

Citation

Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.
Bioinformatics. 2010 Mar 15;26(6):730-6.

Mutalyzer 2.0.34 – HGVS Variant Nomenclature Checker

Mutalyzer 2.0.34

:: DESCRIPTION

Mutalyzer is a tool primarily designed to check descriptions of sequence variants according to the standard human sequence variant nomenclature of the Human Genome Sequence Variation Society (HGVS).

::DEVELOPER

Mutalyzer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Mutalyzer

:: MORE INFORMATION

Citation

An Efficient Algorithm for the Extraction of HGVS Variant Descriptions from Sequences.
Vis JK, Vermaat M, Taschner PE, Kok JN, Laros JF.
Bioinformatics. 2015 Jul 31. pii: btv443.

motifbreakR – Predicting Variant Effects at Transcription Factor Binding Sites

motifbreakR

:: DESCRIPTION

motifbreakR is a package for predicting the disruptiveness Of Single Nucleotide Polymorphisms on transcription factor binding sites.

::DEVELOPER

motifbreakR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

motifbreakR

:: MORE INFORMATION

Citation

motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites.
Coetzee SG, Coetzee GA, Hazelett DJ.
Bioinformatics. 2015 Aug 12. pii: btv470.

famSKAT-RC 20140725 – Combining Family- and Population-based Imputation data for Association analysis of Rare and common Variants in large Pedigrees

famSKAT-RC 20140725

:: DESCRIPTION

famSKAT-RC is an R scripts to carry out a combined rare- and common-variant gene-based test of association in the presence of related individuals.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 famSKAT-RC

:: MORE INFORMATION

Citation:

Genet Epidemiol. 2014 Nov;38(7):579-90. doi: 10.1002/gepi.21844. Epub 2014 Aug 1.
Combining family- and population-based imputation data for association analysis of rare and common variants in large pedigrees.
Saad M1, Wijsman EM.

sapFinder 1.26.0 – Detection of Variant Peptides in Shotgun Proteomics Experiments

sapFinder 1.26.0

:: DESCRIPTION

sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.

::DEVELOPER

 Shaohang Xu <xsh.skye at gmail.com>, Bo Wen <wenbo at genomics.cn>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R
  • BioCOnductor

:: DOWNLOAD

 sapFinder

:: MORE INFORMATION

Citation

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.
Wen B, Xu S, Sheynkman GM, Feng Q, Lin L, Wang Q, Xu X, Wang J, Liu S.
Bioinformatics. 2014 Jul 22. pii: btu397.

sapFinder 1.20.1 – Variant Peptides Detection and Visualization in Shotgun Proteomics.

sapFinder 1.20.1

:: DESCRIPTION

sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.

::DEVELOPER

Shaohang Xu <xsh.skye at gmail.com>, Bo Wen <wenbo at genomics.cn>

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux /Windows / MacOs
  • R
  • BioConductor

:: DOWNLOAD

 sapFinder

:: MORE INFORMATION

Citation

sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments.
Wen B, Xu S, Sheynkman GM, Feng Q, Lin L, Wang Q, Xu X, Wang J, Liu S.
Bioinformatics. 2014 Nov 1;30(21):3136-8. doi: 10.1093/bioinformatics/btu397.

GPViz 1.2.8 – Dynamic Gene-centered Visualization of Genomic Regions and/or Variants

GPViz 1.2.8

:: DESCRIPTION

GPViz (GeneProteinViz) is a versatile Java-based software for dynamic gene-centered visualization of genomic regions and/or variants. User defined data can be loaded in common formats as resulting from analysis workflows used in sequencing applications and studied in the context of the gene, the corresponding transcript isoforms, proteins and their domains or other protein features. Both the genomic regions and variants can be also defined interactively.

::DEVELOPER

the Division of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

GPViz

:: REQUIREMENTS

  • Windows/Linux /MacOsX
  • Java

:: DOWNLOAD

  GPViz

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 1;29(17):2195-6. doi: 10.1093/bioinformatics/btt354. Epub 2013 Jun 19.
GPViz: dynamic visualization of genomic regions and variants affecting protein domains.
Snajder R1, Trajanoski Z, Hackl H.