BOL: Related items

maftools : Summarize, Analyze and Visualize MAF Files

Neel — Wed, 23 Dec 2020 05:29:33 -0600

With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widely accepted and used to store somatic variants detected. The Cancer Genome Atlas Project has sequenced over 30 different cancers with sample size of each cancer type being over 200. Resulting data consisting of somatic variants are stored in the form of Mutation Annotation Format. This package attempts to summarize, analyze, annotate and visualize MAF files in an efficient manner from either TCGA sources or any in-house studies as long as the data is in MAF format.

Address of the bookmark: https://www.bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html

MAJIQ 2 is released !

LEGE — Thu, 09 Jul 2020 03:06:26 -0500

Ability to detect, quantify, and visualize complex and de-novo splicing variations from RNASeq.

MAJIQ’s accuracy compares favorably to other algorithms.

MAJIQ 2 is *way* faster, more memory and I/O efficient

New visualization (VOILA 2.0) Ability to analyze hundreds and thousands of samples Why so negative? (Support for a confident negative set)

Finally, a major reason we are excited about MAJIQ 2.0 is that it sets the code base for many new exciting algorithmic and visualization improvements, with application to new research questions so stay tuned!

More at https://biociphers.wordpress.com/2019/04/01/majiq-2-is-out/

Address of the bookmark: https://majiq.biociphers.org/

Kaiju

Jit — Mon, 27 Jun 2016 11:23:04 -0500

Kaiju is a program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein sequences.

By default, Kaiju uses either the available complete genomes from NCBI RefSeq or the microbial subset of the non-redundant protein database nr used by NCBI BLAST, optionally also including fungi and microbial eukaryotes.

Kaiju translates reads into amino acid sequences, which are then searched in the database using a modified backward search on a memory-efficient implementation of the Burrows-Wheeler transform, which finds maximum exact matches (MEMs), optionally allowing mismatches in the protein alignment. The search can process up to millions of reads per minute using, for example, only 10 GB RAM with a protein database comprising 4821 microbial genomes. Kaiju can also be used for querying any other protein database without taxonomic classification, using either protein or nucleotide queries.

Kaiju is described in Menzel, P. et al. (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7:11257 (open access).

Address of the bookmark: http://kaiju.binf.ku.dk/

Ribbon: Visualizing complex genome alignments and structural variation:

Jit — Wed, 29 Nov 2017 07:40:22 -0600

Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right.

Local installation:

You can install Ribbon locally from Github by following the instructions here: https://github.com/MariaNattestad/Ribbon

Address of the bookmark: http://genomeribbon.com/

GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments

Shruti Paniwala — Mon, 11 Jun 2018 05:43:44 -0500

GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap closure. We demonstrate with sequencing data from various organisms that the gap-closing accuracy of GMcloser is 3–100-fold higher than those of other available tools, with similar efficiency. https://academic.oup.com/bioinformatics/article/31/23/3733/209212

Address of the bookmark: https://academic.oup.com/bioinformatics/article/31/23/3733/209212

dotPlotly: Generate an interactive dot plot from mummer or minimap alignments

Rahul Nayak — Thu, 21 Feb 2019 10:22:17 -0600

Create an interactive dot plot from mummer output OR PAF format

R script that makes a plotly interactive and/or static (png/pdf) dot plot.

Shiny app available for testing

Address of the bookmark: https://github.com/tpoorten/dotPlotly

Bioinformatics approach to Boar Taint

Rahul Agarwal — Wed, 17 Jul 2013 15:50:37 -0500

Meat products obtained from intact male pigs often produce offensive smell or odour which is recognized as a complex genetic trait called boar taint.Androstenone and Skatole in the fat primarily cause boar taint. Metabolism of androstenone and sex steroids share a common pathway which makes removal of boar taint a very challenging task. Castration is a traditional solution to remove boar taint but it also results in bad quality of meat due to low level of steroids which is objectionable to many consumers. Detected functional variant(s) underlying boar taint compounds can be used as genetic markers in selection of male pigs with reduced boar taint levels. Resequencing of a total of 47 samples belong to Norwegian Landrace (NL) and Duroc (D) pigs with varied boar taint levels were done in Illumina HiSeq2000 to >10X average coverage. Short reads generated from these samples mapped to Sus Scrofa version 10.2 reference assembly using Bowtie2. Alignment file then used for calling SNPs and InDels inside previousy identified QTL regions on SSC5,13, and 7 with the aid of FreeBayes , a variant caller tool. A final list of SNPs was prepared after filtering SNPs on the basis of SNP quality, coverage of SNP allele, functional and structural annotation, and repeats, etc. Selected SNPs will be genotyped in sample population for validation and then used for constructing SNPs haplotypes in close linkage disequilibrium with QTLs and fine mapping of QTLs through association mapping of genotyped SNPs.

Genome Browsers

Rahul Agarwal — Fri, 16 Aug 2013 19:04:47 -0500

Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc.

Following are the weblink for different available browsers:

http://www.ensembl.org/index.html

http://ensemblgenomes.org/

http://genome.ucsc.edu/

http://www.ncbi.nlm.nih.gov/genome

http://www.ebi.ac.uk/genomes/

http://flybase.org/

http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi

http://www.sanger.ac.uk/resources/databases/

How Genes are Regulated: Transcription Factors

Thu, 05 Sep 2013 16:54:19 -0500

Each cell in our body inherits the same master copy of DNA, but different cell types use it differently. Transcription Factors help influence which genes are used in which cell. Understanding how these dynamic proteins physically interact with DNA allows us to better understand and model their binding to DNA and their regulation of gene expression. Scientific Direction by the Wasserman Lab at the University of British Columbia: http://www.cmmt.ubc.ca/research/investigators/wasserman/lab Animation and editing by Blair Lyons of Stroma Studios: http://www.stromastudios.com

Molecular Genetics Lecture

Rahul Agarwal — Fri, 27 Sep 2013 04:24:45 -0500

"Robert Sapolsky makes interdisciplinary connections between behavioral biology and molecular genetic influences. He relates protein synthesis and point mutations to microevolutionary change, and discusses conflicting theories of gradualism and punctuated equilibrium and the influence of epigenetics on development theories."

"Robert Sapolsky is an American neuroendocrinologist, professor of biology, neuroscience, and neurosurgery at Stanford University, researcher and author" ----Wikipedia

Address of the bookmark: http://www.youtube.com/watch?v=_dRXA1_e30o