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.

CovaRNA / CovStat 1.16.0 – Detecting Long-range Covariations in Nucleotide Alignments

CovaRNA / CovStat 1.16.0

:: DESCRIPTION

CovaRNA / CovStat is a novel index-based computational method to detect long-range covariation on a genomic scale, as well as for determining the statistical significance of observed covariation patterns in alignment pairs.

::DEVELOPER

Shapiro Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C / R

:: DOWNLOAD

CovaRNA / CovStat 

:: MORE INFORMATION

Citation:

Bindewald E, Shapiro BA.
Computational detection of abundant long-range nucleotide covariation in Drosophila genomes.
RNA. 2013 Sep;19(9):1171-82. doi: 10.1261/rna.037630.112. Epub 2013 Jul 25. PMID: 23887147; PMCID: PMC3753924.

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.

h5vc 2.27.1 – Scalable Nucleotide Tallies with HDF5

h5vc 2.27.1

:: 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.

ntHash 2.0.0 – Recursive Nucleotide Hashing

ntHash 2.0.0

:: 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

Canada’s Michael Smith Genome 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.

BiasAway – A tool to Generate Nucleotide Composition-matched DNA sequences

BiasAway

:: DESCRIPTION

BiasAway is an open-access tool for generating multiple different sequence backgrounds of comparable nucleotide composition relative to a set of input sequences.

::DEVELOPER

Wasserman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 BiasAway

:: MORE INFORMATION

Citation:

Worsley Hunt R, Mathelier A, Del Peso L, Wasserman WW.
Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment.
BMC Genomics. 2014 Jun 13;15(1):472. doi: 10.1186/1471-2164-15-472. PMID: 24927817; PMCID: PMC4082612.

A. Khan, R. Riudavets Puig, P. Boddie, and A. Mathelier.
BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences.
Bioinformatics btaa928 (2020).

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

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.