sefOri 1.0 – Selecting the best engineered sequence features to predict DNA Replication Origins

sefOri 1.0

:: DESCRIPTION

The software sefOri selects the subset of sequence features with the best prediction accuracies of the DNA replication origins for the four yeast genomes.

::DEVELOPER

Health Informatics Lab (HILab)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Python
  • Visual Studio

:: DOWNLOAD

sefOri 

:: MORE INFORMATION

Citation

Bioinformatics. 2019 Jun 20. pii: btz506. doi: 10.1093/bioinformatics/btz506.
sefOri: selecting the best-engineered squence features to predict DNA replication origins.
Lou C, Zhao J, Shi R, Wang Q, Zhou W, Wang Y, Wang G, Huang L, Feng X, Zhou F

AnABlast – Detect potential Coding Regions in DNA by Sequence Comparison

AnABlast

:: DESCRIPTION

AnABlast is an algorithm to discover signals of protein-coding sequences within genomic regions. You can analyze a short nucleotide sequence (up to 25Kb in length or up to 1Mb if you upload the Blast report). It highlights genomic regions with stacked non-significant alignments (protomotifs) which would represent present or ancient protein-coding sequences. It allows to discover new genes in bacteria or exons in eukaryotic organisms.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Methods Mol Biol. 2019;1962:207-214. doi: 10.1007/978-1-4939-9173-0_12.
AnABlast: Re-searching for Protein-Coding Sequences in Genomic Regions.
Rubio A, Casimiro-Soriguer CS, Mier P, Andrade-Navarro MA, Garzón A, Jimenez J, Pérez-Pulido AJ

BioPartsDB – DNA Synthesis Workflow System for Synthetic Biology

BioPartsDB

:: DESCRIPTION

BioPartsDB is an open-source, modular tool for DNA synthesis workflow and parts registration, ready to be used in most scenarios, such as molecular biology laboratories or iGem teams.

::DEVELOPER

BioPartsDB team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BioPartsDB

:: MORE INFORMATION

Citation

BioPartsDB: a synthetic biology workflow web-application for education and research.
Stracquadanio G, Yang K, Boeke JD, Bader JS.
Bioinformatics. 2016 Jul 13. pii: btw394.

GLAD 2.50.0 – Gain and Loss Analysis of DNA

GLAD 2.50.0

:: DESCRIPTION

The GLAD algorithms aims at identifying the chromosomal regions with identical DNA copy number, which are delimited by breakpoints.

::DEVELOPER

U900 Institut Curie – INSERM/Mines ParisTech “Bioinformatics and Computational Systems Biology of Cancer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

 GLAD

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Dec 12;20(18):3413-22. Epub 2004 Sep 20.
Analysis of array CGH data: from signal ratio to gain and loss of DNA regions.
Hupé P, Stransky N, Thiery JP, Radvanyi F, Barillot E.

Jellyfish 2.3.0 – Counting of K-mers in DNA

Jellyfish 2.3.0

:: DESCRIPTION

JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the “compare-and-swap” CPU instruction to increase parallelism.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 JELLYFISH

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Mar 15;27(6):764-70. doi: 10.1093/bioinformatics/btr011. Epub 2011 Jan 7.
A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.
Marçais G, Kingsford C.

Optimizer – A web server utility that optimize a DNA or Protein sequence

Optimizer

:: DESCRIPTION

OPTIMIZER is an on-line PHP application that optimizes the codon usage of a DNA sequence to increase its expression level.

::DEVELOPER

P. Puigbo, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Puigbò P., Guzmán E.Romeu A. and Garcia-Vallvé S. 2007
OPTIMIZER: A web server for optimizing the codon usage of DNA sequences.
Nucleic Acids Research, 35:W126-W131.

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.