iRNA-Methyl / iRNA(m6A)-PseDNC – Identifying N6- methyladenosine sites

iRNA-Methyl /iRNA(m6A)-PseDNC

:: DESCRIPTION

The web-server iRNA-methyl was developed to identify the N6-methyladenosine (m6A). It was observed by the rigorous cross-validation test on the benchmark dataset that the accuracy achieved by the predictor in identifying m6A was 65.59%.

iRNA(m6A)-PseDNC was an updated version of iRNA-Methyl, which was developed to identify the N6-methyladenosine (m6A) in the Saccharomyces cerevisiae genome.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iRNA-Methyl: Identifying N(6)-methyladenosine sites using pseudo nucleotide composition.
Chen W, Feng P, Ding H, Lin H, Chou KC.
Anal Biochem. 2015 Dec 1;490:26-33. doi: 10.1016/j.ab.2015.08.021.

iRNA(m6A)-PseDNC: Identifying N6-methyladenosine sites using pseudo dinucleotide composition.
Chen W, Ding H, Zhou X, Lin H, Chou KC.
Anal Biochem. 2018 Nov 15;561-562:59-65. doi: 10.1016/j.ab.2018.09.002.

iNuc-PseKNC – Predicting Nucleosomes with Pseudo K-tuple Nucleotide Composition

iNuc-PseKNC

:: DESCRIPTION

The web-server iNuc-PseKNC was developed to predict nucleosome occupancy of H. sapiens, C. elegan and D. melanogaster

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition.
Guo SH, Deng EZ, Xu LQ, Ding H, Lin H, Chen W, Chou KC.
Bioinformatics. 2014 Jun 1;30(11):1522-9. doi: 10.1093/bioinformatics/btu083.

SNAPR – Scalable Nucleotide Alignment Program RNA-seq

SNAPR

:: DESCRIPTION

SNAPR is a new method for RNA-seq analysis, optimized for hundreds or even thousands of RNA-seq libraries. SNAPR reads from and writes to BAM format, automatically generates read counts, and accurately identifies viral/bacterial infections and gene fusions.

::DEVELOPER

The Hood-Price Lab for Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • C++

:: DOWNLOAD

 SNAPR

:: MORE INFORMATION

BkTree 20160124 – Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model

BkTree 20160124

:: DESCRIPTION

BkTree is an utility capable of predicting all familites of RNA nucleotide interactions, including base-base, base-phosphate, base-ribose, and base-stacking interactions, from the input query sequence (along with predicted or known canonical Watson-Crick base pairs).

::DEVELOPER

The RNA-Informatics Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BkTree

:: MORE INFORMATION

Citation

Accurate Prediction of RNA Nucleotide Interactions with Backbone k-Tree Model.
Ding L, Xue X, LaMarca S, Mohebbi M, Samad A, Malmberg RL, Cai L.
Bioinformatics. 2015 Apr 16. pii: btv210.

ntHash 1.0.1 – Recursive Nucleotide Hashing

ntHash 1.0.1

:: DESCRIPTION

ntHash is a hashing algorithm tuned for processing DNA/RNA sequences. It performs the best when calculating hash values for adjacent k-mers in an input sequence, operating an order of magnitude faster than the nearest competitors in typical use cases.

::DEVELOPER

Hamid MohamadiGenome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ntHash

:: MORE INFORMATION

Citation

ntHash: recursive nucleotide hashing.
Mohamadi H, Chu J, Vandervalk BP, Birol I.
Bioinformatics. 2016 Jul 16. pii: btw397.

h5vc 2.7.6 – Scalable Nucleotide Tallies with HDF5

h5vc 2.7.6

:: DESCRIPTION

h5vc contains functions to interact with tally data from NGS experiments that is stored in HDF5 files.

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 h5vc

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1464-6. doi: 10.1093/bioinformatics/btu026. Epub 2014 Jan 21.
h5vc: scalable nucleotide tallies with HDF5.
Pyl PT, Gehring J, Fischer B, Huber W.

R3D Align – RNA 3D Structure Alignment

R3D Align

:: DESCRIPTION

R3D Align is a web application for locally optimized, nucleotide to nucleotide pairwise alignments of RNA 3D structure

::DEVELOPER

BGSU RNA Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

R3D Align

:: MORE INFORMATION

Citation

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.
Rahrig RR, Petrov AI, Leontis NB, Zirbel CL.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W15-21. doi: 10.1093/nar/gkt417.

ModelGenerator 0.851 – Amino Acid & Nucleotide Substitution Model Selection

ModelGenerator 0.851

:: DESCRIPTION

ModelGenerator is a model selection program that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

ModelGenerator

:: MORE INFORMATION

Citation:

Thomas M Keane, Christopher J Creevey ,Melissa M Pentony, Thomas J Naughton and James O McInerney (2006)
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified,
BMC Evolutionary Biology, 6:29

SNEP – Simultaneous Detection of Nucleotide and Expression Polymorphisms

SNEP

:: DESCRIPTION

SNEP is a new method that allows simultaneous detection of both nucleotide and expression polymorphisms.

::DEVELOPER

Hironori Fujisawa

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows / MacOSX
  • R

:: DOWNLOAD

 SNEP

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2009 May 6;10:131. doi: 10.1186/1471-2105-10-131.
SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip.
Fujisawa H1, Horiuchi Y, Harushima Y, Takada T, Eguchi S, Mochizuki T, Sakaguchi T, Shiroishi T, Kurata N.

Correlation Finder – Seek Correlations between Nucleotides in Genomic Sequences

Correlation Finder

:: DESCRIPTION

Correlation Finder is a free software which allows to seek correlations between nucleotides in genomic sequences. It computes some parameters for each analyzed correlation: the relative abundance, the conditional probability, the frequency of the words making up the correlation.

::DEVELOPER

Gruppo di Biologia Computazionale

:: SCREENSHOTS

Correlation

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Correlation Finder

:: MORE INFORMATION

Citation:

In Silico Biol. 2005;5(5-6):465-8.
Correlation Finder.
Piva F1, Principato G.