jMOTU 1.0.7 / Taxonerator 0.9 – Analysis of Large DNA Barcode Datasets

jMOTU 1.0.7 / Taxonerator 0.9

:: DESCRIPTION

jMOTU is a software package for clustering barcode DNA sequence data into molecular operational taxonomic units (MOTU).

Taxonnerator is a software package for carrying out simple similarity-based annotation of clustered barcode sequence data produced by jMOTU. It generates taxonomic annotation for MOTU by BLASTing representative sequences against a preformatted database of sequences from known organisms (available from this website). Taxonnerator is useful for initial taxonomic investigation of environmental barcode datasets. For each database sequence showing significant similarity to a MOTU, taxonomic information is stored at all taxonomic levels.

::DEVELOPER

The Blaxter Lab at The Institute of Evolutionary Biology University of Edinburgh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

jMOTUTaxonerator

:: MORE INFORMATION

Citation

PLoS One. 2011 Apr 25;6(4):e19259. doi: 10.1371/journal.pone.0019259.
jMOTU and Taxonerator: turning DNA Barcode sequences into annotated operational taxonomic units.
Jones M1, Ghoorah A, Blaxter M.

iDNA4mC – Identifying DNA 4-methylcytosine sites

iDNA4mC

:: DESCRIPTION

iDNA4mC is the first webserver to identify 4mC sites, in which DNA sequences are encoded with both nucleotide chemical properties and nucleotide frequency.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iDNA4mC: identifying DNA N4-methylcytosine sites based on nucleotide chemical properties.
Chen W, Yang H, Feng P, Ding H, Lin H.
Bioinformatics. 2017 Nov 15;33(22):3518-3523. doi: 10.1093/bioinformatics/btx479.

iDNA6mA-PseKNC – Identifying DNA N6-methyladenosine sites

iDNA6mA-PseKNC

:: DESCRIPTION

iDNA6mA-PseKNC is a DNA 6mA (N6-methyladenosine sites) predictor that is established by incorporating nucleotide physicochemical properties into Pseudo K-tuple Nucleotide Composition (PseKNC).

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC.
Feng P, Yang H, Ding H, Lin H, Chen W, Chou KC.
Genomics. 2019 Jan;111(1):96-102. doi: 10.1016/j.ygeno.2018.01.005.

i6mA-Pred – Identifying DNA N6-methyladenine Sites in the Rice Genome

i6mA-Pred

:: DESCRIPTION

i6mA-Pred web server was developed to identify DNA N6-methyladenine (6mA) sites in the rice gemome. The results of jackknife test based on the benchmark dataset indicates that the current predictor may become a useful high-throughput tool in identifying 6mA sites.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

i6mA-Pred: identifying DNA N6-methyladenine sites in the rice genome.
Chen W, Lv H, Nie F, Lin H.
Bioinformatics. 2019 Aug 15;35(16):2796-2800. doi: 10.1093/bioinformatics/btz015.

DNASIZE – Computation of size of DNA and Protein Fragments from Their Electrophoretic Mobility

DNASIZE

:: DESCRIPTION

DNASIZE allows to compute the length of DNA or protein fragments from its electropheric mobility using a graphical method.

::DEVELOPER

G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • DOS

:: DOWNLOAD

  DNASIZE 

:: MORE INFORMATION

Citation

Raghava, G. P. S. (2001)
A web server for computing size of DNA/Protein fragment using graphical method.
Biotech Software and Internet Report 2:198-200.

MUMmer 4.0.0Beta2 / pymummer 0.11.0 – Alignment of Large-scale DNA & Protein Sequences

MUMmer 4.0.0Beta2/ pymummer 0.11.0

:: DESCRIPTION

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.

pymummer is Python3 module for running MUMmer and reading the output

::DEVELOPER

MUMmer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC / Python

:: DOWNLOAD

MUMmer, pymummer

:: MORE INFORMATION

MUMmer is now an open source project.

Citation:

MUMmer4: A fast and versatile genome alignment system
G. Marçais , A.L. Delcher, A.M. Phillippy, R. Coston, S.L. Salzberg, A. Zimin,
PLoS computational biology (2018), 14(1): e1005944.

LedPred 1.7.7 – Learning from DNA to Predict enhancers

LedPred 1.7.7

:: DESCRIPTION

LedPred aims at creating a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, next-generation sequencing (NGS) peaks and signals and other numerical scores of the sequences using supervised classification.

::DEVELOPER

Elodie Darbo, Denis Seyres, Aitor Gonzalez<aitor.gonzalez at univ-amu.fr>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R/ BioConductor

:: DOWNLOAD

 LedPred

:: MORE INFORMATION

Citation:

LedPred: An R/Bioconductor package to predict regulatory sequences using support vector machines.
Seyres D, Darbo E, Perrin L, Herrmann C, González A.
Bioinformatics. 2015 Dec 1. pii: btv705

tantan 22 – Find Cryptic Repeats in DNA, RNA, and Protein Sequences.

tantan 22

:: DESCRIPTION

tantan is a tool to mask simple regions (low complexity and short-period tandem repeats) in DNA, RNA, and protein sequences.The aim of tantan is to prevent false predictions when searching for homologous regions between two sequences. Simple repeats often align strongly to each other, causing false homology predictions.

::DEVELOPER

Martin C. Frith

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 tantan

:: MORE INFORMATION

Citation

MC Frith,
A new repeat-masking method enables specific detection of homologous sequences,
Nucleic Acids Research 2011 39(4):e23.

GenScalpel 1.1 – Retrieve and Extract DNA or Protein sequence from NCBI GenBank file

GenScalpel 1.1

:: DESCRIPTION

GenScalpel is a program designed for specified-sequence retrieval and extraction from large-scale sequence sets in NCBI GenBank flatfile format.

::DEVELOPER

GenScalpel team

:: SCREENSHOTS

GenScalpel

:: REQUIREMENTS

  • Windows / Linux
  • Perl

:: DOWNLOAD

 GenScalpel

:: MORE INFORMATION

Citation

J Hered. 2012 Nov-Dec;103(6):908-11. doi: 10.1093/jhered/ess052. Epub 2012 Sep 2.
GenScalpel: an application for sequence retrieval and extraction from the GenBank flatfile.
Yin YH, Du LM, Yue BS.

DR_bind1 – DNA and RNA Binding Residue Prediction Server

DR_bind1

:: DESCRIPTION

DR_bind1 can be used to predict the DNA-binding residues for a given protein chain.

::DEVELOPER

The Institute of Biomedical Sciences, Academia Sinica

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 Feb;42(3):e15. doi: 10.1093/nar/gkt1299. Epub 2013 Dec 16.
Identifying RNA-binding residues based on evolutionary conserved structural and energetic features.
Chen YC, Sargsyan K, Wright JD, Huang YS, Lim C.