miRNAFold – Ab initio miRNA Precursor Search in Genomes

miRNAFold

:: DESCRIPTION

miRNAFold is a fast ab-initio algorithm for searching for pre-miRNA precursors in genomes.

::DEVELOPER

EVRY RNA – IBISC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

miRNAFold: a web server for fast miRNA precursor prediction in genomes.
Tav C, Tempel S, Poligny L, Tahi F.
Nucleic Acids Res. 2016 May 29. pii: gkw459.

Nucleic Acids Res. 2012 Jun;40(11):e80. doi: 10.1093/nar/gks146. Epub 2012 Feb 22.
A fast ab-initio method for predicting miRNA precursors in genomes.
Tempel S1, Tahi F.

MaGnET 2.0 – Malaria Genome Exploration Tool

MaGnET 2.0

:: DESCRIPTION

MaGnET is a software tool enabling intuitive ‘exploration-style’ visualization of functional genomics data relating to the malaria parasite, Plasmodium falciparum.

::DEVELOPER

MaGnET team

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Java

:: DOWNLOAD

MaGnET

:: MORE INFORMATION

Citation:

Bioinformatics. 2013 Sep 15;29(18):2350-2. doi: 10.1093/bioinformatics/btt384. Epub 2013 Jul 27.
MaGnET: Malaria Genome Exploration Tool.
Sharman JL1, Gerloff DL.

L_RNA_scaffolder – Long Transcriptome Reads to Scaffold Genome

L_RNA_scaffolder

:: DESCRIPTION

L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to scaffold genome fragments.

::DEVELOPER

L_RNA_scaffolder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler
Perl

:: DOWNLOAD

L_RNA_scaffolder

:: MORE INFORMATION

Citation:

BMC Genomics. 2013 Sep 8;14:604. doi: 10.1186/1471-2164-14-604.
L_RNA_scaffolder: scaffolding genomes with transcripts.
Xue W1, Li JT, Zhu YP, Hou GY, Kong XF, Kuang YY, Sun XW.

DNAcompact 20130829 – Genome Compression algorithm with/without Reference

DNAcompact 20130829

:: DESCRIPTION

DNA-COMPACT is a software of DNA COMpression based on a pattern-aware contextual modeling technique.

::DEVELOPER

DNAcompact team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

DNAcompact

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 25;8(11):e80377. doi: 10.1371/journal.pone.0080377. eCollection 2013.
DNA-COMPACT: DNA COMpression based on a pattern-aware contextual modeling technique.
Li P1, Wang S, Kim J, Xiong H, Ohno-Machado L, Jiang X.

AutoEditor 1.20 – Automated Correction of Genome Sequence Errors

AutoEditor 1.20

:: DESCRIPTION

AutoEditor is a tool for correcting sequencing and basecaller errors using sequence assembly and chromatogram data. On average AutoEditor corrects 80% of erroneous base calls, with an accuracy of 99.99%.This in turn improves the overall accuracy of genome sequences and facilitates the use of these sequences for polymorphism discovery.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

AutoEditor

:: MORE INFORMATION

Citation

“Automated correction of genome sequence errors.”
Gajer P, Schatz M, Salzberg SL,
Nucleic Acids Research, 2004. 32(2):562-9.

Genomedata 1.3.5 – Storage of Multiple Tracks of Numeric data Anchored to Genome

Genomedata 1.3.5

:: DESCRIPTION

Genomedata is a format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint.

::DEVELOPER

Noble Research Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Python

:: DOWNLOAD

Genomedata

:: MORE INFORMATION

Citation:

Hoffman MM, Buske OJ, Noble WS. 2010.
The Genomedata format for storing large-scale functional genomics data.
Bioinformatics, 26(11):1458-1459; doi:10.1093/bioinformatics/btq164

YGAP – Yeast Genome Annotation Pipeline

YGAP

:: DESCRIPTION

YGAP is an online tool to annotate yeast species based on sequence and synteny conservation.

::DEVELOPER

the Wolfe Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 17;13:237. doi: 10.1186/1471-2105-13-237.
A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach.
Proux-Wéra E1, Armisén D, Byrne KP, Wolfe KH.

LIAN 3.7 – Testing Genome-Wide Linkage Equilibrium From Multilocus Data

LIAN 3.7

:: DESCRIPTION

LIAN is a program to test the null hypothesis of linkage equilibrium for multilocus data.

::DEVELOPER

Bernhard Haubold

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

LIAN

:: MORE INFORMATION

Citation

Bioinformatics. 2000 Sep;16(9):847-8.
LIAN 3.0: detecting linkage disequilibrium in multilocus data. Linkage Analysis.
Haubold B1, Hudson RR.

DISCOVAR 51750 – Genome Shotgun Assembler and Variant Caller

DISCOVAR 51750

:: DESCRIPTION

DISCOVAR is a whole genome shotgun assembler and variant caller that can generate high quality assemblies and variant calls from the latest 250 base Illumina PCR-free fragment reads.

::DEVELOPER

Computational Research and Development Group, Broad Institute of MIT and Harvard

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
GCC
SAMtools

:: DOWNLOAD

DISCOVAR

:: MORE INFORMATION

BAIT 1.4 – Organizing Genomes and Mapping Rearrangements in Single Cells

BAIT 1.4

:: DESCRIPTION

BAIT (Bioinformatic Analysis of Inherited Templates) is a software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

::DEVELOPER

Terry Fox Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
SAMtools
BEDtools
R
DNAcopy R package
gplots R package.

:: DOWNLOAD

BAIT

:: MORE INFORMATION

Citation

Genome Med. 2013 Sep 13;5(9):82.
BAIT: Organizing genomes and mapping rearrangements in single cells.
Hills M1, O’Neill K, Falconer E, Brinkman R, Lansdorp PM.