KAT 2.1.1 – K-mer Analysis Toolkit

 DNA / Genome Analysis 89 views Comments Off on KAT 2.1.1 – K-mer Analysis Toolkit
Aug 102016
 
KAT 2.1.1 - K-mer Analysis Toolkit

KAT 2.1.1 :: DESCRIPTION KAT is a suite of tools that analyse jellyfish kmer hashes. ::DEVELOPER The Genome Analysis Centre (TGAC) :: SCREENSHOTS N/a :: REQUIREMENTS Linux Java jellyfish :: DOWNLOAD  KAT :: MORE INFORMATION

MethylMix 1.6.0 – Identifying DNA Methylation Driven Genes

 DNA / Genome Analysis 79 views Comments Off on MethylMix 1.6.0 – Identifying DNA Methylation Driven Genes
Aug 102016
 
MethylMix 1.6.0 - Identifying DNA Methylation Driven Genes

MethylMix 1.6.0 :: DESCRIPTION MethylMix is an algorithm implemented in R to identify disease specific hyper and hypomethylated genes. ::DEVELOPER Olivier Gevaert <olivier.gevaert at gmail.com> :: SCREENSHOTS N/A :: REQUIREMENTS Linux/ Windows /MacOsX R BioConductor / Matlab :: DOWNLOAD  MethylMix , for Matlab :: MORE INFORMATION Citation Bioinformatics. 2015 Jan 20. pii: btv020. [Epub ahead of print] […]

MOODS 1.9.2 – MOtif Occurrence Detection Suite

 DNA / Genome Analysis 289 views Comments Off on MOODS 1.9.2 – MOtif Occurrence Detection Suite
Aug 102016
 
MOODS 1.9.2 - MOtif Occurrence Detection Suite

MOODS 1.9.2 :: DESCRIPTION MOODS ( MOtif Occurrence Detection Suite) is a suite of algorithms for matching position weight matrices (PWM) against DNA sequences. It features advanced matrix matching algorithms implemented in C++ that can be used to scan hundreds of matrices against chromosome-sized sequences in few seconds. ::DEVELOPER Pasi Rastas :: SCREENSHOTS N/A :: […]

PcircRNA_finder – circRNA Prediction in Plants

 RNA Analysis 16 views Comments Off on PcircRNA_finder – circRNA Prediction in Plants
Aug 082016
 
PcircRNA_finder - circRNA Prediction in Plants

PcircRNA_finder :: DESCRIPTION PcircRNA_finder is a software for circRNA prediction in plants. ::DEVELOPER PcircRNA_finder team :: SCREENSHOTS N/A :: REQUIREMENTS Linux / MacOsX Perl Python :: DOWNLOAD  PcircRNA_finder :: MORE INFORMATION Citation: PcircRNA_finder: a software for circRNA prediction in plants. Chen L, Yu Y, Zhang X, Liu C, Ye C, Fan L. Bioinformatics. 2016 Aug […]

Metaxa2 2.1.3 – Identification and Classification of Small Subunit (SSU) rRNA Sequences

 RNA Analysis 211 views Comments Off on Metaxa2 2.1.3 – Identification and Classification of Small Subunit (SSU) rRNA Sequences
Aug 082016
 
Metaxa2 2.1.3 - Identification and Classification of Small Subunit (SSU) rRNA Sequences

Metaxa2 2.1.3 :: DESCRIPTION Metaxa2 is a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets ::DEVELOPER Johan Bengtsson :: SCREENSHOTS N/A :: REQUIREMENTS Linux / MacOsX :: DOWNLOAD   Metaxa2 :: MORE INFORMATION Citation: Mol Ecol Resour. 2015 […]

FARAO – The Flexible All-Round Annotation Organizer

 Miscellaneous 12 views Comments Off on FARAO – The Flexible All-Round Annotation Organizer
Aug 082016
 
FARAO – The Flexible All-Round Annotation Organizer

FARAO 1.0b :: DESCRIPTION FARAO is the Flexible All-Round Annotation Organizer, a set of software tools that constitute as a highly configurable way to handle sequence annotation and coverage information. ::DEVELOPER Johan Bengtsson :: SCREENSHOTS N/A :: REQUIREMENTS Linux  / MacOsX Perl :: DOWNLOAD  FARAO :: MORE INFORMATION Citation: FARAO – The Flexible All-Round Annotation Organizer. […]

TriMetAss 1.2 – The Trinity-based Iterative Metagenomics Assembler

 Assembly Tools 75 views Comments Off on TriMetAss 1.2 – The Trinity-based Iterative Metagenomics Assembler
Aug 082016
 
TriMetAss 1.2 – The Trinity-based Iterative Metagenomics Assembler

TriMetAss 1.2 :: DESCRIPTION TriMetAss is an extension to the Trinity software , which can assemble select regions surrounding interesting features in metagenomic data ::DEVELOPER Johan Bengtsson :: SCREENSHOTS N/A :: REQUIREMENTS Linux  / MacOsX Java Trinity :: DOWNLOAD  TriMetAss :: MORE INFORMATION Citation: Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Shotgun […]

partiFold – Transmembrane Beta-barrel Proteins Predictor

 Protein Sequence Analysis 324 views Comments Off on partiFold – Transmembrane Beta-barrel Proteins Predictor
Aug 082016
 
partiFold - Transmembrane Beta-barrel Proteins Predictor

partiFold / partiFold-Align :: DESCRIPTION partiFold is a software to investigate the folding landscape of TMBs (Transmembrane Beta-barrel Proteins). partiFold-Align is the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm’s complexity is polynomial in time and space. ::DEVELOPER Jerome Waldispühl , Bonnie Berger :: SCREENSHOTS N/A :: REQUIREMENTS Linux /  Mac OsX […]

CsSNP 1.1 – Comparative Synteny SNPs Detector

 DNA / Genome Analysis 10 views Comments Off on CsSNP 1.1 – Comparative Synteny SNPs Detector
Aug 082016
 
CsSNP 1.1 - Comparative Synteny SNPs Detector

CsSNP 1.1 :: DESCRIPTION CsSNP is a freely available web tool based on the Blat, Blast, and Perl programs to detect comparative segments SNPs and to show the detail information of SNPs. ::DEVELOPER CsSNP team :: SCREENSHOTS N/A :: REQUIREMENTS Web browser :: DOWNLOAD   NO :: MORE INFORMATION Citation: CsSNP: A Web-Based Tool for the […]

MirCompare – Algorithm to Compare Plant and Mammalian miRNAs

 RNA Analysis 16 views Comments Off on MirCompare – Algorithm to Compare Plant and Mammalian miRNAs
Aug 082016
 
MirCompare - Algorithm to Compare Plant and Mammalian miRNAs

MirCompare :: DESCRIPTION MirCompare is an innovative algorithm developed to compare sets of microRNAs belonging to different kingdoms, for their capacity to bind host mRNAs. ::DEVELOPER MirCompare team :: SCREENSHOTS N/A :: REQUIREMENTS Web browser :: DOWNLOAD   NO :: MORE INFORMATION Citation: Bioinformatics Prediction and Experimental Validation of MicroRNAs Involved in Cross-Kingdom Interaction. Pirrò […]