BOL: Related items

Pathway Analysis

Rahul Agarwal — Fri, 03 Oct 2014 08:51:13 -0500

Pathway Analysis is usually performed with aim to enrich the genes with their functional information and reveal the underlying biological mechanisms pursue by genes. Pathway Analysis is not only limited to what biological pathways a particular set of expressed genes follow but also to disclose the relationships between these genes. With availability of more genomics, transcriptomics and proteomics data, interactions between genes involve in multiple pathways become more clear and also relationships between the genes, their transcripts, and their gene products. However, existing tools and dbs mainly based on knowledge driven approach in which pathways will be identified by finding the correlation between the information in one of the pathway knowledge databases (KEGG,Reactome,Panther,BioCarta, Panther,GO,NCI,WikiPathways,etc) and gene expression result for a specific conditions for instance tumor, obesity , cold resistant crops/plants, etc.

Introductory Articles/ppt/sources:

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002375

http://bioinformatics.mdanderson.org/MicroarrayCourse/Lectures09/Pathway%20Analysis.pdf

http://gettinggeneticsdone.blogspot.de/2012/03/pathway-analysis-for-high-throughput.html

http://davetang.org/muse/tag/pathway/

https://www.biostars.org/p/42219/

http://bioinformatics.ca//files/public/Pathways_2014_Module4_v2.pdf

http://bioinformatics.ca//files/public/Pathways_2014_Module2.pdf

Impotant Database and Tools:

GeneMANIA, Cytoscape, IPA and Metacore (Commerical ), Pathway Commons, Reactome ,Panther, BioCyc, WikiPathways, Pathvisio, KEGG, NCI, Stringdb, Amigo, WebGestalt ,ConsensusPathDB ,GSEA,Blast2go

Popular R based tools:

Reactome.db, ReactomePA, ClusterProfiler, Gage, SPIA, topGO, Pathview,DOSE,GOStat

More:

http://www.bioconductor.org/help/search/index.html?q=Enrichment+analysis+

CovCal: Coverage / Read Count Calculator

Jit — Wed, 15 Jun 2016 18:08:13 -0500

Coverage / Read Count Calculator

Calculate how much sequencing you need to hit a target depth of coverage (or vice versa).

Instructions: set the read length/configuration and genome size, then select what you want to calculate.

Written by Stephen Turner, based on the Lander-Waterman formula, inspired by a similar calculator written by James Hadfield. Coverage is calculated as C=LN/G and reads as N=CG/L where C = Coverage (X),L = Read length (bp), G = Haploid genome size (bp), and N = Number of reads. Source code on GitHub.

Address of the bookmark: http://apps.bioconnector.virginia.edu/covcalc/

Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome

Jit — Wed, 29 Nov 2017 05:08:53 -0600

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr (https://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads, as existing packages were incapable of assembling the long read lengths (5-50kbp) at such high error rate (between ~5 and 40% error). With this new method we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: the contig N50 length is more than ten-times greater than an Illumina-only assembly (678kb versus 59.9kbp), and has greater than 99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.

Address of the bookmark: http://schatzlab.cshl.edu/data/nanocorr/

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Poonam Mahapatra — Mon, 26 Aug 2019 18:07:33 -0500

Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast, Saccharomyces cerevisiae, has many isolates currently being sequenced with long reads.

Address of the bookmark: https://github.com/yjx1217/LRSDAY

Entire Human Genome Sequencing !

LEGE — Tue, 02 Apr 2024 01:19:29 -0500

Cost-effective whole human genome sequencing has revolutionized the landscape of genetic research and personalized medicine by making comprehensive genetic analysis accessible to a wider population. Through advancements in sequencing technologies, such as next-generation sequencing (NGS), costs have significantly decreased, enabling researchers and healthcare providers to analyze an individual's complete genetic makeup with greater efficiency and affordability. This has profound implications for disease diagnosis, prognosis, and treatment, as it allows for the identification of genetic predispositions and the customization of healthcare interventions based on an individual's unique genetic profile. Moreover, as the cost continues to decline, the potential for population-scale genomic studies and large-scale screening programs becomes increasingly feasible, promising to further enhance our understanding of human genetics and improve healthcare outcomes on a global scale.

Here are few companies:

https://mynucleus.com/

https://myome.com/

https://nebula.org/whole-genome-sequencing-dna-test/

Structure of Binary files used for storing sequencing data-bam and sff

Rahul Agarwal — Sun, 11 Aug 2013 14:29:49 -0500

Many times bioinformatician needs to parse binary files like bam and sff. Advantage of binary files is that they occupy less space in memory with maximum information content.

Link for those who looking for structure of Bam and sff file:

Bam:

http://samtools.sourceforge.net/SAMv1.pdf (from page 12)

sff file (for Ion torrent and 454 files):

http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff

Binary file Editor and Viewer:

http://mh-nexus.de/en/hxd/

Bioinformatics and Sequencing Courses and Workshops

Rahul Agarwal — Sat, 24 Aug 2013 16:41:26 -0500

Swiss Institute of Bioinformatics (SIB) organises lots of bioinformatics courses covering wide range of topics:

http://www.isb-sib.ch/education/training-courses.html

Canadian bioinformatics also organises various bioinformatics and sequencing courses:

http://bioinformatics.ca/workshops

In addition to above two, EMBI Europe, EMBO Europe, Cold Spring Harbour USA, Wellcome Trust UK and NOVA Europe also organise bioinformatics and sequencing courses annually:

http://www.embl.de/training/events/index.php?p_outstation=ALL

http://www.embo.org/funding-awards/courses-workshops

http://meetings.cshl.edu/courses.html

http://www.wellcome.ac.uk/Education-resources/Courses-and-conferences/Advanced-Courses-and-Scientific-Conferences/Advanced-Courses/index.htm

http://www.nova-university.org/pagetop.cfm?MenySidorTop_id=2&open=7

Illuminating next generation sequencing data with Go

Rahul Agarwal — Fri, 23 Aug 2013 07:13:33 -0500

Another good lecture for Illumina sequencing data analysis from

Dan Kortschak, Bioinformatics Group, School of Molecular and Biomedical Science ,The University of Adelaide

Address of the bookmark: http://talks.biogo.googlecode.com/git/illumination/illumination.pdf

Tigers genome sequenced

Rahul Agarwal — Tue, 17 Sep 2013 16:48:24 -0500

Fifteen scientists led by Dr Jong Bhak of Genome Research Foundation, South Korea, decoded as many as 3 billion nucleotides (organic molecules that form the basic building blocks of nucleic acids, such as DNA). They identified 20,000 genes related to various functions of the tiger.

The biggest and perhaps most fearsome of the world's big cats, the tiger, shares 95.6 percent of its DNA with humans' cute and furry companions, domestic cats.

The new research showed that big cats have genetic mutations that enabled them to be carnivores. The team also identified mutations that allow snow leopards to thrive at high altitudes.

Reference:

http://www.nbcnews.com/science/your-cat-ferocious-tigers-share-lot-95-6-percent-their-4B11182690

http://timesofindia.indiatimes.com/home/environment/flora-fauna/Gene-mapping-of-tiger-completed/articleshow/22671681.cms

Paper:

http://www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html

Biggest Human Brain Project (HBP) launched!!!

Rahul Agarwal — Mon, 07 Oct 2013 19:50:55 -0500

"In neuroscience, the project will use neuroinformatics and brain simulation to collect and integrate experimental data, identifying and filling gaps in our knowledge, and prioritising future experiments.

In medicine, the HBP will use medical informatics to identify biological signatures of brain disease, allowing diagnosis at an early stage, before the disease has done irreversible damage, and enabling personalized treatment, adapted to the needs of individual patients. Better diagnosis, combined with disease and drug simulation, will accelerate the discovery of new treatments, drastically lowering the cost of drug discovery.

In computing, new techniques of interactive supercomputing, driven by the needs of brain simulation, will impact a vast range of industries. Devices and systems, modelled after the brain, will overcome fundamental limits on the energy-efficiency, reliability and programmability of current technologies, clearing the road for systems with brain-like intelligence."

Source: http://www.forbes.com/sites/jenniferhicks/2013/10/07/the-human-brain-project-begins/

(https://www.facebook.com/humanbrainproj/info)

Home Page:

https://www.humanbrainproject.eu/

Jobs:

https://www.humanbrainproject.eu/participate/jobs