:: DESCRIPTION
6mA-Finder is a novel online tool for predicting DNA N6-methyladenine sites in genomes.
::DEVELOPER
Bioinformatics and Systems Medicine Laboratory
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Xu H, Hu R, Jia P, Zhao Z.
6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes.
Bioinformatics. 2020 May 1;36(10):3257-3259. doi: 10.1093/bioinformatics/btaa113. PMID: 32091591; PMCID: PMC7214014.
:: DESCRIPTION
Deep4mC is a web server of systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning.
::DEVELOPER
Bioinformatics and Systems Medicine Laboratory
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Xu H, Jia P, Zhao Z.
Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning.
Brief Bioinform. 2021 May 20;22(3):bbaa099. doi: 10.1093/bib/bbaa099. PMID: 32578842; PMCID: PMC8138820.
:: DESCRIPTION
repDNA (Representations of DNAs) is a Python package for generating the widely used features reflecting the physicochemical properties and sequence-order effects of DNAs and nucleotides.
::DEVELOPER
Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects.
Liu B, Liu F, Fang L, Wang X, Chou KC.
Bioinformatics. 2014 Dec 10. pii: btu820.
:: DESCRIPTION
RANDNA is a free software which allows to create random DNA sequences setting both their length and the percentage of nucleotide composition.
::DEVELOPER
Gruppo di Biologia Computazionale
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
In Silico Biol. 2006;6(3):253-8.
RANDNA: a random DNA sequence generator.
Piva F1, Principato G.
:: DESCRIPTION
IR takes as input a DNA squence and returns the global index of repetitiveness, Ir.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2006 Dec 22;7:541.
How repetitive are genomes?
Haubold B1, Wiehe T.
:: DESCRIPTION
PhyloGibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms. Many existing approaches to either search for sequence-motifs that are overrepresented in the input data, or for sequence-segments that are more conserved evolutionary than expected. PhyloGibbs combines these two approaches and identifies significant sequence-motifs by taking both over-representation and conservation signals into account.
PhyloGibbs-MP is a significant enhancement.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Rahul Siddharthan, Eric D. Siggia, and Erik van Nimwegen
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
PLoS Comput Biol 1(7): e67 2005
:: DESCRIPTION
PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
PANDASEQ-SAM is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. This version works on SAM/BAM formatted files.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Andre P Masella, Andrea K Bartram, Jakub M Truszkowski, Daniel G Brown and Josh D Neufeld.
PANDAseq: paired-end assembler for illumina sequences.
BMC Bioinformatics 2012, 13:31.
:: DESCRIPTION
Sequedex classifies DNA sequences by analyzing collections of sequences in new ways.
::DEVELOPER
The Sequedex Team
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Joel Berendzen et al.
Rapid phylogenetic and functional classification of short genomic fragments with signature peptides
BMC Research Notes 2012, 5:460 doi:10.1186/1756-0500-5-460
:: DESCRIPTION
UVWORD determines the number of times that each DNA word present in a sequence (target) is found in a second sequence (source), a procedure that we have called oligonucleotide profiling.
::DEVELOPER
Bioinformatics Unit, Instituto de Biomedicina de Valencia (CSIC) / Universidad de Valencia
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Res Notes. 2008 Feb 28;1:5. doi: 10.1186/1756-0500-1-5.
Fast comparison of DNA sequences by oligonucleotide profiling.
Arnau V1, Gallach M, Marín I.
:: DESCRIPTION
CSSSCL is a python package that uses Combined Sequence Similarity Scores for accurate taxonomic CLassification of long and short reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
CSSSCL: a python package that uses Combined Sequence Similarity Scores for accurate taxonomic CLassification of long and short sequence reads.
Borozan I, Ferretti V.
Bioinformatics. 2015 Oct 9. pii: btv587.
