BOL: Related items

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.

Want to Know which genome assembler rule the world ?

Rahul Agarwal — Sun, 11 Aug 2013 11:42:32 -0500

Assemblathon 2: evaluating de novo methods of genome assembly

http://www.gigasciencejournal.com/content/2/1/10/abstract

http://blogs.nature.com/news/2013/07/genome-assembly-contest-prompts-soul-searching.html

http://assemblathon.org/post/44431915644/feedback-and-analysis-of-the-assemblathon-2-p

Latest paper on comparison of mapping tools

Rahul Agarwal — Tue, 03 Sep 2013 18:00:38 -0500

A. Hatem, D. Bozdag, A. E. Toland, U. V. Catalyurek "Benchmarking short sequence mapping tools" BMC Bioinformatics, 14(1):184, 2013.

http://bmi.osu.edu/hpc/software/benchmark/

http://bmi.osu.edu/hpc/software/pmap/pmap.html

Other similiar papers:

http://online.liebertpub.com/doi/pdf/10.1089/cmb.2012.0022

http://bioinformatics.oxfordjournals.org/content/28/24/3169

Some new Mapping tool links:

GSNAP

http://research-pub.gene.com/gmap/

RMAP

http://rulai.cshl.edu/rmap/

mrsFAST

http://mrsfast.sourceforge.net/Home

http://sourceforge.net/projects/mrsfast/files/mrsfast-ultra-3.1.0/

BFAST

http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page

SHRiMP (for AB SOLiD color-space reads)

http://compbio.cs.toronto.edu/shrimp/

RazerA 3

http://www.seqan.de/projects/razers/

Address of the bookmark: http://www.biomedcentral.com/1471-2105/14/184

Bio-Rad Acquires GnuBIO

Rahul Agarwal — Sat, 19 Apr 2014 10:36:36 -0500

http://www.businesswire.com/news/home/20140411005331/en/Bio-Rad-Acquires-GnuBIO-Developer-Droplet-Based-DNA-Sequencing#.U1KXnPm1b8o

Deadly Human Pathogen Cryptococcus Sequenced

Rahul Agarwal — Fri, 25 Apr 2014 11:02:21 -0500

"Now, researchers have sequenced the entire genome and all the RNA products of the most important pathogenic lineage of Cryptococcus neoformans, a strain called H99. The results, which appear in PLOS Genetics, also describe a number of genetic changes that can occur after laboratory handling of H99 that make it more susceptible to stress, hamper its ability to sexually reproduce and render it less virulent."

Source:

http://www.biosciencetechnology.com/news/2014/04/deadly-human-pathogen-cryptococcus-fully-sequenced

Paper:

http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004292

Genomics and sequencing approach for identification of biomarkers to assess the efficacy of TGF-βRI inhibitors (of liver cancer) in vivo

Rahul Agarwal — Tue, 05 Aug 2014 13:55:32 -0500

Liver cancer is third leading cause of deaths and fourth most frequent occuring cancer worldwide. There are multiple signaling pathways responsible for causing cancer amongst which TGFb is most important cytokine whose signaling pathway promote cancer. However, main problem is to cure this cancer at late stage where we still have no treatment strategy to tackle this deadly cancer. Hence we need to find out new therapeutic target. One way is to look the relationships between mRNA, methylation and miRNA data of patients with different pathological conditions (cancer vs control either with inhibitor/not). MiRNA is small RNA molecules known to inhibit mRNA expression of particular gene by binding improperly to 3'UTR region of a gene and hence block binding of TF /translation of gene. CpG regions is known to located at promoter region of gene (5' UTR) and usually hypomethylated which allow to gene to transcribe and translate however sometime this region become hyper-methylated thats prevent expression of host gene. Thus , integration of these three data reveal new targets and pathways important for causing or preventing cancer and also reveal biomarker thats check the effects of inhibitor on signaling pathway underlying liver cancer.

Scaffolding of a bacterial genome using MinION nanopore sequencing

Rahul Agarwal — Tue, 07 Jul 2015 16:59:25 -0500

Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot be easily resolved. A new generation of sequencers offering substantially longer reads is emerging, notably the Pacific Biosciences (PacBio) RS II system and the MinION system, released in early 2014 by Oxford Nanopore Technologies through an early access program.

Address of the bookmark: http://www.nature.com/srep/2015/150707/srep11996/full/srep11996.html

Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator

Jit — Wed, 24 May 2017 08:41:41 -0500

Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file.

Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, metaproteomic shotgun and amplicon datasets from current sequencing technologies such as Sanger, 454, Illumina. These simulated datasets can be used to test the accuracy of bioinformatic tools under specific hypothesis, e.g. with or without sequencing errors, or with low or high community diversity. Grinder may also be used to help decide between alternative sequencing methods for a sequence-based project, e.g. should the library be paired-end or not, how many reads should be sequenced.

Address of the bookmark: https://sourceforge.net/projects/biogrinder/files/biogrinder/

Earth BioGenome Project

Jit — Wed, 25 Apr 2018 07:48:56 -0500

The central goal of the Earth BioGenome Project is to understand the evolution and organization of life on our planet by sequencing and functionally annotating the genomes of 1.5 million known species of eukaryotes, a massive group that includes plants, animals, fungi and other organisms whose cells have a nucleus that houses their chromosomal DNA. To date, the genomes of less than 0.2 percent of eukaryotic species have been sequenced.

More at https://www.ucdavis.edu/news/earth-biogenome-project-aims-sequence-dna-all-complex-life

Choosing the Right NGS Sequencing Instrument for Your Study

Neel — Wed, 15 Jun 2022 00:37:29 -0500

The right sequencing instrument for your study depends on your project goal. Setting aside turnaround time and price, it essentially comes down to the numbers of reads and read length you need for your experiment. Below, we've described and compared metrics for each of the instruments available. If you’re new to high-throughput sequencing and have questions about how you should design your sequencing run, fill out our free consultation form and we'll get in touch with you to help.

More at https://genohub.com/ngs-instrument-guide/

Address of the bookmark: https://genohub.com/ngs-instrument-guide/