BOL: Related items

KisSplice

Jit — Tue, 16 Aug 2016 08:34:19 -0500

KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads.

KisSplice is not a full-length transcriptome assembler. This means that it will output the variable regions of the transcripts, not reconstruct them entirely.

KisSplice comes as a workflow, with several possible post-treatments meant to facilitate the analysis of the results. The choice of the post-treatment depends on the availability of a reference genome/transcriptome and on the need to perform a differential analysis, as summarised in the following table.

Address of the bookmark: http://kissplice.prabi.fr/

4DGenome

Jitendra Narayan — Mon, 04 Jul 2016 00:44:55 -0500

Records in 4DGenome are compiled through comprehensive literature curation of experimentally-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted interactions in 5 organisms. Experimental data cover both high throughput datasets and individiual focused studies.

All interaction data are freely available in a standardized file format. Records can be queried by genomic regions, gene names, organism, and detection technology.

Address of the bookmark: http://4dgenome.research.chop.edu/

OrganellarGenomeDRAW

Jit — Tue, 16 Aug 2016 08:13:13 -0500

OrganellarGenomeDRAW is dedicated to convert genetic information stored in GenBank entries to graphical maps. The input text file has to be in GenBank flat file format, whereas the output format can be chosen among several formats. The application is especially optimized and adapted for the creation of high-quality, detailed circular maps of organellar genomes like the plastid genome (plastome) or the mitochondrial genome (chondriome). Nevertheless, you can upload any GenBank entry. The workflow is devided into three steps.

More at http://ogdraw.mpimp-golm.mpg.de/cgi-bin/ogdraw.pl

Address of the bookmark: http://ogdraw.mpimp-golm.mpg.de/index.shtml

vcfR

Archana Malhotra — Fri, 19 Aug 2016 07:38:24 -0500

Most variant calling pipelines result in files containing large quantities of variant information. The variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in the vignette ‘vcf data.’ These files are typically intended to be post-processed (i.e., filtered) as an attempt to remove false positives or otherwise problematic sites. The R package vcfR provides tools to facilitate this filtering as well as to visualize the effects of choices made during this process.

Address of the bookmark: https://cran.r-project.org/web/packages/vcfR/vignettes/visualization_1.html

GeneValidator - Identify problems with predicted genes

Poonam Mahapatra — Fri, 26 Aug 2016 06:00:03 -0500

GeneValidator helps in identifing problems with gene predictions and provide useful information extracted from analysing orthologs in BLAST databases. The results produced can be used by biocurators and researchers who need accurate gene predictions.

If you would like to use GeneValidator on a few sequences, see our online GeneValidator Web App -http://genevalidator.sbcs.qmul.ac.uk.

If you use GeneValidator in your work, please cite us as follows:

Dragan M‡, Moghul MI‡, Priyam A, Bustos C & Wurm Y. 2016. GeneValidator: identify problems with protein-coding gene predictions. Bioinformatics, doi: 10.1093/bioinformatics/btw015.

Address of the bookmark: https://github.com/wurmlab/genevalidator

Sushi: An R/Bioconductor package for visualizing genomic data

Jit — Wed, 31 Aug 2016 08:29:12 -0500

Sushi: An R/Bioconductor package for visualizing genomic data

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/Sushi/inst/doc/Sushi.pdf

CIRCOS Visualize !!

Jit — Fri, 02 Sep 2016 08:29:26 -0500

Before uploading a data file, check the samples gallery to make sure that your data format is compatible.

Your file must be plain text.
Your data values must be non-negative integers.
Data must be space-separated (one or more tab or space, which will be collapsed).
No two rows or columns may have the same name.
Column and row names must begin with a letter (e.g. 'A', 'A0', 'A-0') and can only contain letters, numbers and _. No punctuation!
Maximum row + column total is 150 — if exceeded, rows and columns are limited to 75.
If you are using order, size and color rows/columns in combination they must appear in that order.

Need help? Post questions to the Circos Google Group.

http://mkweb.bcgsc.ca/tableviewer/visualize/

Address of the bookmark: http://mkweb.bcgsc.ca/tableviewer/visualize/

Sybil

Jit — Wed, 07 Sep 2016 03:20:44 -0500

The Sybil software package provides a primarily web-based front-end to comparative genome datasets warehoused in a chado relational database. It was developed by the bioinformatics department at The Institute for Genomic Research (TIGR) and development continues at the J. Craig Venter Institute (JCVI) and the Institute for Genome Sciences (IGS) at the University of Maryland: Baltimore. Sybil has been used at TIGR/JCVI, IGS, NYU, New York Medical College, Novartis Vaccines and University of Maryland: College Park to support a number of research projects that involve comparative genome analysis. The following sections provide some high-level technical details about the overall architecture and external dependencies of the Sybil package.

Address of the bookmark: http://sybil.sourceforge.net/

CGView - Circular Genome Viewer

Jit — Mon, 19 Sep 2016 07:52:26 -0500

GView is a Java package used to display and navigate bacterial genomes. GView is useful for producing high-quality genome maps for use in publications and websites, or as a visualization tool in a sequence annotation pipeline. Users can interact with the genome using a powerful pan-and-zoom interface, or GView can write static images of a genome to a file. GView can draw a genome using either circular or linear layouts. For examples of some of the images GView can produce, see the Image Gallery. GView is a re-write of CGView, a circular genome viewer written by Paul Stothard. The goal of GView is to provide greater user interaction, and more flexibility in how the genome map is rendered. To aid with easily configuring the display of a genome, a style editor has been included to provide an intuitive, user-friendly graphical user interface for customizing genome maps. Styling attributes such as colours or fonts for the various map elements can be adjusted in real time. Customized styles can be saved for later use or for application to other genome maps using GView's custom file format.

Address of the bookmark: http://wishart.biology.ualberta.ca/cgview/

Murasaki

Anjana — Fri, 30 Sep 2016 10:22:30 -0500

Murasaki is an anchor alignment program that is

exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 35 wall minutes), or 8 mammals in 21 CPU hours (42 wall minutes))
scalable (Arbitrarily parallelizable across multiple nodes using MPI)
memory efficient. (Even a single node with 16GB of ram can handle over 1Gbp of sequence)
unlimited by pattern length or selection
repeat tolerant

Address of the bookmark: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?Murasaki