mCross – Modeling RBP Binding Specificity by registering protein-RNA Crosslink Sites

mCross

:: DESCRIPTION

mCrossBase is a database of RNA-binding protein (RBP) binding motifs and crosslink sites defined jointly from CLIP data using a novel algorithm mCross

::DEVELOPER

Zhang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Feng et al. (2019),
Modeling the in vivo specificity of RNA-binding proteins by precisely registering protein-RNA crosslink sites.
Mol Cell. 74:1189-1204.E6.

AIRlINER – Assessment of A-to-I RNA Editing Sites in Non-repetitive Regions

AIRlINER

:: DESCRIPTION

AIRlINER is an algorithmic approach to the assessment of A-to-I  (Adenosine-to-Inosine)  RNA editing sites in non-repetitive regions. It determines the editing probability of an adenosine by analyzing its flanking region of 10 nucleotides. Such pattern is then combined with a similar model calculated from un-edited sequences, resulting in the estimation of an unbiased editing probability.

::DEVELOPER

AIRlINER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Knowledge in the Investigation of A-to-I RNA Editing Signals.
Nigita G, Alaimo S, Ferro A, Giugno R, Pulvirenti A.
Front Bioeng Biotechnol. 2015 Feb 24;3:18. doi: 10.3389/fbioe.2015.00018.

SFselect – Learning Natural Selection from the Site Frequency Spectrum

SFselect

:: DESCRIPTION

SFselect is a method for classifying genomic regions evolving under positive selection, from those evolving neutrally

::DEVELOPER

Roy Ronen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SFselect

:: MORE INFORMATION

Citation

Genetics. 2013 Sep;195(1):181-93. doi: 10.1534/genetics.113.152587. Epub 2013 Jun 14.
Learning natural selection from the site frequency spectrum.
Ronen R, Udpa N, Halperin E, Bafna V.

PCI-SS – PCI-Based Protein Scondary Structure Site Prediction Server

PCI-SS

:: DESCRIPTION

PCI-SS is a method of predicting protein secondary structure using a PCI-based classifier and also a consensus method to combine PCI with PSIPRED.

::DEVELOPER

Green lab at Carleton University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Green, J.R., Korenberg, M.J., and Aboul-Magd, Md., 2009,
PCI-SS: MISO dynamic nonlinear protein secondary structure prediction
BMC Bioinformatics 2009, 10:222 doi:10.1186/1471-2105-10-222

GPS-YNO2 1.0.1 – Prediction of Tyrosine Nitration Sites

GPS-YNO2 1.0.1

:: DESCRIPTION

GPS-YNO2 is a software package to predict PTN sites. The software demonstrated a promising accuracy of 76.51%, a sensitivity of 50.09% and a specificity of 80.18% from the leave-one-out validation.

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

:: REQUIREMENTS

  • WIndows / Linux / MacOsX
  • Java

:: DOWNLOAD

 GPS-YNO2

:: MORE INFORMATION

Citation

GPS-YNO2: Computational prediction of tyrosine nitration sites in proteins
Zexian Liu, Jun Cao, Qian Ma, Xinjiao Gao, Jian Ren and Yu Xue.
Molecular BioSystems, 2011, 7(4): 1197-1204

TTS mapping – Triplex Target DNA Site Mapping

TTS mapping

:: DESCRIPTION

TTS mapping is a web-based search engine to find and annotate pTTSs within human genome region of interest. The engine provides descriptive statistics of pTTSs in a given region and its sequence context. Different annotation tracks of TTS-overlapping gene region(s), G-quadruplex motifs, CpG Island, miRNA precursors, miRNA targets, transcription factor binding sites (TFBSs), Single Nucleotide Polymorphisms (SNPs), small nucleolar RNAs (snoRNA), and repeat elements are also mapped based on sequence location provided by UCSC genome browser, G-quadruplex database and several other datasets.

::DEVELOPER

the Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2009 Dec 3;10 Suppl 3:S9. doi: 10.1186/1471-2164-10-S3-S9.
TTS mapping: integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome.
Jenjaroenpun P1, Kuznetsov VA.

AdaPatch 1.0 – Searche for Dense and Spatially Distinct Clusters of sites

AdaPatch 1.0

:: DESCRIPTION

AdaPatch searches for dense and spatially distinct clusters of sites under positive selection on the surface of proteins.

::DEVELOPER

Algorithmic Bioinformatics, Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  AdaPatch

:: MORE INFORMATION

Citation

Christina Tusche, Lars Steinbrück and Alice C. McHardy
Detecting Patches of Protein Sites of Influenza A Viruses under Positive Selection
Mol Biol Evol (2012) 29 (8): 2063-2071.

MCMCcodonsite – Identify Sites under Positive Selection

MCMCcodonsite

:: DESCRIPTION

 MCMCcodonsite is a program implementing some codon models allowing \omega = d_N/d_S to vary among sites (M0, M2a, M3, M7, M8) in a Bayesian framework

::DEVELOPER

The Aris-Brosou lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • PAML

:: DOWNLOAD

 MCMCcodonsite

:: MORE INFORMATION

Citaion

Aris-Brosou, S. 2006.
Identifying sites under positive selection with uncertain parameter estimates.
Genome. 49:767-776.

GZ-gamma – Estimate Parameter of Substitution Rate Variation among Sites

GZ-gamma

:: DESCRIPTION

GZ-gamma is designed to estimate the expected number of substitutions of each amino acid (nucleotide) site, and the gamma shape parameter for the rate variation among sites, using a combination of ancestral sequence inference and maximum likelihood estimation when the phylogenetic relationships of these homologous sequences are known.

::DEVELOPER

Jianzhi Zhang ,  Xun Gu 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  GZ-gamma

:: MORE INFORMATION

Citation:

Gu, X. and J. Zhang J (1997)
A simple method for estimating the parameter of substitution rate variation among sites.
Mol. Biol. Evol. 14:1106-1113