Tag: Transform

TSpred – Predict Substitutions that Transform Query Protein Sequence/structure into Temperature-sensitive Mutant

TSpred

:: DESCRIPTION

TSpred attempts to identify a small set of amino acid residues in a query protein that have a high probability of being buried (side-chain accessibilities less than 5%, expressed in terms of residue depth). The server suggests substitutions at these buried positions that are most likely to result in a temperature sensitive (Ts) phenotype.

::DEVELOPER

Bioinformatics Institute of Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2014 Apr 29. [Epub ahead of print]
TSpred: a web server for the rational design of temperature-sensitive mutants.
Tan KP1, Khare S, Varadarajan R, Madhusudhan MS.

TransFIC – Transformed Functional Impact score for Cancer

TransFIC

:: DESCRIPTION

TransFIC is a method to transform Functional Impact scores taking into account the differences in basal tolerance to germline SNVs of genes that belong to different functional classes. This transformation allows to use the scores provided by well-known tools (e.g. SIFT, Polyphen2, MutationAssessor) to rank the functional impact of cancer somatic mutations. Mutations with greater transFIC are more likely to be cancer drivers.

::DEVELOPER

 The Biomedical Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 TransFIC

:: MORE INFORMATION

Citation

Abel Gonzalez-Perez, Jordi Deu-Pons and Lopez-Bigas N.
Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.
Genome Medicine. 2012. 4:89 doi:10.1186/gm390.

PBWT – Implementation of Positional Burrows-Wheeler Transform for Genetic data

PBWT

:: DESCRIPTION

The pbwt package provides a core implementation and development environment for PBWT (Positional Burrows-Wheeler Transform) methods for storing and computing on genome variation data sets.

::DEVELOPER

Richard Durbin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 pbwt

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 1;30(9):1266-72. doi: 10.1093/bioinformatics/btu014. Epub 2014 Jan 9.
Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT).
Durbin R.

BW4SA – Burrows-Wheeler Transform for Sequence Analysis

BW4SA

:: DESCRIPTION

BW4SA is a generic, practical, versatile library for implementing a variety of (bio)sequence analysis algorithms in succinct space.

::DEVELOPER

GSA (Genome-scale algorithmics) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BW4SA

:: MORE INFORMATION

Citation

Djamal Belazzougui, Fabio Cunial, Juha Kärkkäinen, Veli Mäkinen
Versatile succinct representations of the bidirectional Burrows-Wheeler transform.
ESA 2013, Springer, Lecture Notes in Computer Science Volume 8125, 2013, pp 133-144

GTOOL 0.7.5 – Transform Sets of Genotype Data for use with SNPTEST and IMPUTE

GTOOL 0.7.5

:: DESCRIPTION

GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.

::DEVELOPER

Colin Freeman ,  Jonathan Marchini

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

   GTOOL 

:: MORE INFORMATION

 

SWATH2stats 1.22.0 – Transform and Filter SWATH Data for Statistical Packages

SWATH2stats 1.22.0

:: DESCRIPTION

SWATH2stats is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.

::DEVELOPER

Aebersold Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R / BioConductor

:: DOWNLOAD

 SWATH2stats

:: MORE INFORMATION

Citation

PLoS One. 2016 Apr 7;11(4):e0153160. doi: 10.1371/journal.pone.0153160. eCollection 2016.
SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.
Blattmann P, Heuse M, Aebersold R.

DeepInsight – Transform Non-image data to Image

DeepInsight

:: DESCRIPTION

DeepInsight converts non-image samples into a well-organized image-form. Thereby, the power of convolution neural network (CNN), including GPU utilization, can be realized for non-image samples. Furthermore, DeepInsight enables feature extraction through the application of CNN for non-image samples to seize imperative information and shown promising results.

::DEVELOPER

Laboratory for Medical Science Mathematics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

DeepInsight

:: MORE INFORMATION

Citation

Sci Rep. 2019 Aug 6;9(1):11399. doi: 10.1038/s41598-019-47765-6.
DeepInsight: A methodology to transform a non-image data to an image for convolution neural network architecture.
Sharma A, Vans E, Shigemizu D, Boroevich KA, Tsunoda T.

STR_ConvertFormats 20120306 – Transform STR typing data to Genotyper table format

STR_ConvertFormats 20120306

:: DESCRIPTION

STR_ConvertFormats is an Excel-based tool developed to transform STR typing data from tables where every row contains information from a single locus (e.g., GeneMapperID output format) to a format where every row contains all typing results for a single sample (e.g., Genotyper table format).

::DEVELOPER

Dave Duewer at National Institute of Standards and Technolog

:: SCREENSHOTS

:: REQUIREMENTS

  • Excel

:: DOWNLOAD

STR_ConvertFormats

:: MORE INFORMATION

Citation

See description in Becky Hill presentation at the Expert Systems Workshop held in conjunction with the 2nd Annual Present and Future Technological Advances in Human Identification Conference (Roanoke, VA), March 27, 2006, “NIST Experience with FSS-i3 software“