RESOURCESRESOURCES

Deep Sequencing Tool Kit

Tools and resources for the analysis of next generation sequence data, including publically available NGS databases.

AnnoJ

http://www.annoj.org/

Anno-J is a Web 2.0 application designed for visualizing deep sequencing data and other genome annotation data. It is web-based and with a simple interface. An easy to navigate manual is online

Galaxy-UK

http://galaxy-community.org.uk/

The central resource for UK-specific Galaxy issues and events aims to:

  • Bring the Galaxy community in the United Kingdom closer together
  • Identify and address the needs of the community
  • Encourage interaction and collaboration.

 

IGB -Integrated Genome Browser

http://bioviz.org/igb/

The Integrated Genome Browser (IGB, pronounced Ig-Bee) is an interactive, zoomable, scrollable software program you can use to visualize and explore genome-scale data sets, such as tiling array data, next-generation sequencing results, genome annotations, microarray designs, and the sequence itself.

MPSS

http://mpss.udel.edu/at/

Contains Arabidopsis MPSS (massively parallel signature sequencing) expression data along with databases for 'Parallel analysis of RNA ends', small RNA, and DN methylation. Other plant species, including medicago and maize, are also supported. 

Plant microRNA database (PMRD)

http://bioinformatics.cau.edu.cn/PMRD/

Database integrating plant microRNAs data, consisting of microRNA sequence and their target genes, secondary dimension structure and other information. 

From the abstract: The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser

UCSG Genome Browser

http://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks?clade=plant&org=A.+thaliana&db=araTha1&c=chr5&position=chr5%3A3172000-3180999&pix=800&ruler=full&rulerBaseZoom=3x&dinkL=2.0&dinkR=2.0&textSize=small&guidelines=0&leftLabels=1&centerLabels=1&trackControlsOnMain=1&hgt_configGroupTarget=none&chromInfo=full&hgt.baseShowAsm=1&hgt.baseShowPos=1&hgt.baseTitle_araTha1=&hgt.motifs=CG&hgt.motifComplement=1&oligoMatch=dense&hgt.oligoMatch=cg&cutters=hide&hgt.cutters=&hgFind.matches=

Display of any requested portion of genomes at any scale, together with dozens of aligned annotation tracks (known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal bands, mouse homologies, and more). Half of the annotation tracks are computed at UCSC from publicly available sequence data. The remaining tracks are provided by collaborators worldwide. Users can also add their own custom tracks to the browser for educational or research purposes.

WMD web microRNA designer

http://wmd2.weigelworld.org/cgi-bin/mirnatools.pl

Web-tool for the automated design of artificial microRNAs. There is also a useful help page containing background information and an introduction to microRNAs.