FRST 1.2 – Protein Model Quality Estimation Method

FRST 1.2

:: DESCRIPTION

FRST serves to validate the energy of a protein structure. The server computes both an overall and a per-residue energy profile of a protein structure. The energy profile can be visualized in different ways, including a per-residue plot and a colored structure representation, accessible as a series of dynamic web pages.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FRST

:: MORE INFORMATION

Citation:

Silvio C.E. Tosatto.
The Victor/FRST Function for Model Quality Estimation.
Journal of Computational Biology 2005; 12(10):1316-1327

ChiLin 2.1 – ChIP-seq Data quality and Analysis Pipeline

ChiLin 2.1

:: DESCRIPTION

ChiLin provides a more flexible handle for understanding the ChIP-seq analysis workflow.

::DEVELOPER

X. Shirley Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 ChiLin

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2016 Oct 3;17(1):404.
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.
Qin Q, et al.

QUALITY 1.1.6 – Variant of the minimum Chi-squared method for limiting Dilution Assays

QUALITY 1.1.6

:: DESCRIPTION

The program QUALITY is a variant of the minimum Chi-squared (MC) method for limiting dilution assays, and for which he has demonstrated by simulation desirable properties of minimum variance (i.e., high precision) and minimum bias. Our method modifies the MC method to allow the user to specify the probabilities of a false negative and false positive PCR.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

QUALITY

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 QUALITY

:: MORE INFORMATION

Citation

AIDS Res Hum Retroviruses. 1997 Jun 10;13(9):737-42.
Quantitation of target molecules from polymerase chain reaction-based limiting dilution assays.
Rodrigo AG1, Goracke PC, Rowhanian K, Mullins JI.

SQPR 8.01 – Sequence Quality Plate Reader

SQPR 8.01

:: DESCRIPTION

SQPR is a graphical interface software to allow the researcher to view and assess the quality of sequencing results using a series of program scripts developed to process data generated by automated sequencers.

::DEVELOPER

Gerard R. Lazo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Perl
  • CGI

:: DOWNLOAD

 SQPR

:: MORE INFORMATION

Citation

Lazo, G.R., Tong, J., Miller, R., Hsia, C., Rausch, C., Kang, Y., and Anderson, O.D. 2001.
Software scripts for quality checking of high-throughput nucleic acid sequencers.
BioTechniques 30(6):1300-1305.

ProQ2 / ProQM – Membrane Protein / Protein Quality Predictor

ProQ2 / ProQM

:: DESCRIPTION

ProQ2 (Protein Quality Predictor) is a neural network based predictor that based on a number of structural features predicts the quality of a protein model. ProQ is optimized to find correct models in contrast to other methods which are optimized to find native structures.

ProQM method uses a support vector machine with a combination of general and membrane protein-specific features.

::DEVELOPER

IFM Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ProQ2 / ProQM

:: MORE INFORMATION

Citation:

ProQ2: Estimation of Model Accuracy Implemented in Rosetta.
Uziela K, Wallner B.
Bioinformatics. 2016 Jan 5. pii: btv767.

Improved model quality assessment using ProQ2.
Arjun Ray, Erik Lindahl and B. Wallner.
BMC Bioinformatics 2012, 13:224, doi:10.1186/1471-2105-13-224

Bioinformatics. 2010 Dec 15;26(24):3067-74. doi: 10.1093/bioinformatics/btq581. Epub 2010 Oct 14.
Model quality assessment for membrane proteins.
Ray A, Lindahl E, Wallner B.

Qualiseq 20150216 – Quality Genomic Sequence Retrieval

Qualiseq 20150216

:: DESCRIPTION

QualiSeq is a Quality Genomic Sequence Retrieval Tool.

::DEVELOPER

Qualiseq team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Yu-Chang Cheng, Tz-Chao Lin, Kuo-His Lee, Yan-Hau Chen, Ming-Fang Tsai, Yi-Jung Lin, and Adam Yao (2006)
Qualiseq: Quality Genomic Sequence Retrieval,
Journal of Genetics and Molecular Biology Vol. 17, No. 4, 204-210, December 1, 2006

BIGpre 2.0.2 – Quality Assessment software for both Illumina and 454 platforms

BIGpre 2.0.2

:: DESCRIPTION

BIGpre is a quality assessment package for next-genomics sequencing data

::DEVELOPER

BIGpre team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BIGpre

:: MORE INFORMATION

Citation

Genomics Proteomics Bioinformatics. 2011 Dec;9(6):238-44. doi: 10.1016/S1672-0229(11)60027-2.
BIGpre: a quality assessment package for next-generation sequencing data.
Zhang T1, Luo Y, Liu K, Pan L, Zhang B, Yu J, Hu S.

CuReSim / CuReSimEval – Customized Read Simulator / Evaluate Mapping Quality of CuReSim Simulated Reads

CuReSim 1.2 / CuReSimEval 1.1

:: DESCRIPTION

CuReSim is a customized tool which generates synthetic New-Generation Sequencing reads, supporting read simulation for major letter-base sequencing platforms.

CuReSimEval is a tool to evaluate the mapping quality of the CuReSim simulated reads.

::DEVELOPER

CuReSim team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/ Linux
  • Java

:: DOWNLOAD

 CuReSim , CuReSimEval

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Apr 5;15:264. doi: 10.1186/1471-2164-15-264.
Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.
Caboche S1, Audebert C, Lemoine Y, Hot D.

UrQt 1.0.17 – Unsupervised Quality Trimming for NGS data

UrQt 1.0.17

:: DESCRIPTION

UrQt is a new quality control method for Unsupervised Quality trimming of Next Generation Sequencing reads

:: DEVELOPER

The Biometry and Evolutionary Biology laboratory (LBBE)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 UrQt

:: MORE INFORMATION

Citation

UrQt: an efficient software for the Unsupervised Quality trimming of NGS data
Modolo L, Lerat E.
BMC Bioinformatics. 2015 Apr 29;16(1):137.

Coval 1.5 – Improving the Quality of Short Read Alignment data

Coval 1.5

:: DESCRIPTION

Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads, thereby increasing the calling accuracy of currently available tools for SNP and indel identification.

::DEVELOPER

Coval team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl

:: DOWNLOAD

 Coval 

:: MORE INFORMATION

Citation

Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.
Kosugi S, Natsume S, Yoshida K, MacLean D, Cano L, Kamoun S, Terauchi R.
PLoS One. 2013 Oct 8;8(10):e75402. doi: 10.1371/journal.pone.0075402