Tag: Subtype

Spial – Analysis of Subtype-specific Features in multiple Sequence Alignments of Proteins

Spial

:: DESCRIPTION

Spial (Specificity in alignments) is a web-server that takes a pair of multiple sequence alignments as input and produces an output that highlights positions which are conserved in both alignments (the consensus), and positions which are specific to either alignment.

::DEVELOPER

Spial team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Nov 15;26(22):2906-7. doi: 10.1093/bioinformatics/btq552. Epub 2010 Sep 29.
Spial: analysis of subtype-specific features in multiple sequence alignments of proteins.
Wuster A1, Venkatakrishnan AJ, Schertler GF, Babu MM.

CNALR 1.0 – Stratification of Tumour Subtypes based on Copy Number Alteration Profiles

CNALR 1.0

:: DESCRIPTION

CNALR is an R package to perform a stratification of tumour subtypes based on copy number alteration profiles using next-generation sequence data. This webpage is currently set to support the submission of the manuscript Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data

::DEVELOPER

Arief Gusnanto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 CNALR

:: MORE INFORMATION

Citation

Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data.
Gusnanto A, Tcherveniakov P, Shuweihdi F, Samman M, Rabbitts P, Wood HM.
Bioinformatics. 2015 Apr 5. pii: btv191.

hiBRCApCR 1.0 – Predicting pCR for Breast Cancer Subtypes

hiBRCApCR 1.0

:: DESCRIPTION

hiBRCApCR is a software for accurate prediction of neoadjuvant chemotherapy pathological complete remission (pCR) for the four sub-types of breast cancer.

::DEVELOPER

Health Informatics Lab (HILab)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Python

:: DOWNLOAD

hiBRCApCR

:: MORE INFORMATION

GLaD – A Mixed-Membership Model for Heterogenous Tumor Subtype Classification

GLaD

:: DESCRIPTION

GLAD is a mixed-membership classification model that simultaneously learns a sparse biomarker signature for each subtype as well as a distribution over subtypes for each sample.

::DEVELOPER

Flaherty Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

  GLaD

:: MORE INFORMATION

Citation

GLAD: A mixed-membership model for heterogeneous tumor subtype classification.
Saddiki H, McAuliffe J, Flaherty P.
Bioinformatics. 2014 Sep 29. pii: btu618.

MethylAction – Detecting Differentially Methylated Regions (DMRs) that distinguish Biological and Disease subtypes

MethylAction

:: DESCRIPTION

MethylAction is an R package for detecting differentially methylated regions (DMRs) from enrichment-based techniques for sequencing DNA methlyation genome-wide.

::DEVELOPER

Jeff Bhasin,  in the Ting Lab at the Cleveland Clinic Genomic Medicine Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

 MethylAction

:: MORE INFORMATION

Citation

MethylAction: detecting differentially methylated regions that distinguish biological subtypes.
Bhasin JM, Hu B, Ting AH.
Nucleic Acids Res. 2016 Jan 8;44(1):106-16. doi: 10.1093/nar/gkv1461.

PrimerHunter 1.0.2 – Primer Design for PCR-Based Virus Subtype Identification

PrimerHunter 1.0.2

:: DESCRIPTION

PrimerHunter is a tool for selecting highly sensitive and specific primers for virus subtyping. It takes as input sets of both target and non-target sequences and ensures that selected primers amplify all target sequences and none of the non-target sequences by relying on accurate melting temperature computations based on the nearest-neighbor model of Santalucia and the fractional programming algorithm of  Leber et al.

PrimerHunter Online version

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PrimerHunter

:: MORE INFORMATION

Citation:

J. Duitama and D.M. Kumar and E. Hemphill and M. Khan and I.I. Mandoiu and C.E. Nelson,
PrimerHunter: A Primer Design Tool for PCR-Based Virus Subtype Identification,
Nucleic Acids Research 37, pp. 2483-2492, 2009