BOL: Related items

Roth Lab

Tue, 11 Mar 2014 17:43:45 -0500

The Roth Lab seeks insight into biological systems through genome- and proteome-scale experimentation and analysis.

Current computational interests:

Systematic analysis of genetic epistasis to identify redundant or compensatory systems and to reveal order of action in genetic pathways.
Using knockout, knockdown, or overexpression, or other perturbation experiments in combinations of genes in S. cerevisiae, C. elegans or mouse.
Using genome-scale genotyping of natural polymorphisms in S. cerevisiae and human populations.
Alternative splicing and its relationship to protein interaction networks.
Integrating large-scale studies including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns to quantitatively assign function to genes and guide experimentation.

More at http://llama.mshri.on.ca/index.html

The 8000 years old Tibetian gene mutation !!!

Neel — Wed, 20 Aug 2014 21:57:44 -0500

A new study has provided insight into how gene mutation around 8,000 years ago helped Tibetans' to survive in the thin air on the Tibetan Plateau, where an average elevation is of 14,800 feet.

A study led by University of Utah scientists is the first to find a genetic cause for the adaptation, a single DNA base pair change that dates back 8,000 years and demonstrate how it contributes to the Tibetans' ability to live in low oxygen conditions.

About 8,000 years ago, the gene EGLN1 changed by a single DNA base pair. Today, a relatively short time later on the scale of human history, 88 percent of Tibetans have the genetic variation, and it was virtually absent from closely related lowland Asians. The findings indicate the genetic variation endows its carriers with an advantage.

In those without the adaptation, low oxygen caused their blood to become thick with oxygen-carrying red blood cells, an attempt to feed starved tissues, which could cause long-term complications such as heart failure. The researchers found that the newly identified genetic variation protected Tibetans by decreasing the over-response to low oxygen.

Reference: http://www.nature.com/nature/journal/v512/n7513/abs/nature13408.html

Genetic code - Amino Acid

Poonam Mahapatra — Sun, 26 Oct 2014 07:45:58 -0500

The genetic code consists of 64 triplets of nucleotides. These triplets are called codons.With three exceptions, each codon encodes for one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code: most of the amino acids being encoded by more than one codon.

The image summarise all in one.

More at http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html

seqloc 0.6

Gudiya Pal — Sun, 28 Dec 2014 12:51:29 -0600

The Bio.SeqLoc modules in seqloc are designed to represent positions and locations (ranges of positions) on sequences, particularly nucleotide sequences. My original motivation for writing these packages was handing the locations of genes in eukaryotic genomes.

Handle sequence locations for bioinformatics http://www.ingolia-lab.org/seqloc-tutorial.html

Address of the bookmark: http://www.stackage.org/snapshot/nightly-2014-12-28/package/seqloc-0.6

Scripted DNA !!!

Jit — Mon, 17 Aug 2015 17:44:04 -0500

As per bioinformatician DNA is partially scripted ;) You dont believe in it. Please have a look at image carefully:)

Genome Browser : GBrowse

Jit — Fri, 19 Feb 2016 09:22:43 -0600

Generic Genome Browser Version 2: A Tutorial for Administrators

This is an extensive tutorial to take you through the main features and gotchas of configuring GBrowse as a server. This tutorial assumes that you have successfully set up Perl, GD, BioPerl and the other GBrowse dependencies. If you haven't, please see the GBrowse HOWTO During most of the tutorial, we will be using the "in-memory" GBrowse database (no relational database required!) Later we will show how to set up a genome size database using the berkeleydb and MySQL adaptors.

More at http://elp.ucdavis.edu/tutorial/tutorial.html

Address of the bookmark: http://elp.ucdavis.edu/tutorial/tutorial.html

Strudel

Anjana — Fri, 30 Sep 2016 09:47:02 -0500

Strudel is our graphical tool for visualizing genetic and physical maps of genomes for comparative purposes. The application aims to let the user examine their data at a variety of different levels of resolution, from entire maps to individual markers, and explore syntenic relationships between genomes. All browsing and interaction with Strudel happens in real-time – there is no need to wait while the maps are generated. It is built using Java 1.6 and ships with its own JRE, so there is no need for users to install or update Java.

Address of the bookmark: https://ics.hutton.ac.uk/strudel/

MIRO : miRNA omics

Jit — Tue, 04 Oct 2016 14:50:48 -0500

The MIRO (the miRNA omics) pipeline is a flexible and powerful tool for the analysis of miRNA (or more generall short RNA) expression using short-read deep sequencing data. In its present implementation MIRO is especially adapted for the analysis of reads generated with the Illumina sequencing platform. MIRO allows to preprocess the Solexa-reads, map them flexibly to several reference genomes using one of four different mappers, create differential gene (miRNA) expression profiles and cluster reads using one of several algorithm. MIRO output is furthermore compatible with software such as genome browsers and miRDeep.

Address of the bookmark: http://seq.crg.es/download/software/Miro/

GenomeRing: alignment visualization based on SuperGenome coordinates

Neel — Wed, 18 Jan 2017 10:24:10 -0600

The number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. Such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions, deletions or from rearrangement events. Computational tools that can visualize genome alignments in a meaningful manner are needed to help researchers gain new insights into the underlying data. Such visualizations typically are either realized in a linear fashion as in genome browsers or by using a circular approach, where relationships between genomic regions are indicated by arcs. Both methods allow for the integration of additional information such as experimental data or annotations. However, providing a visualization that still allows for a quick and comprehensive interpretation of all important genomic variations together with various supplemental data, which may be highly heterogeneous, remains a challenge.

More at https://academic.oup.com/bioinformatics/article/28/12/i7/268598/GenomeRing-alignment-visualization-based-on

Address of the bookmark: http://it.informatik.uni-tuebingen.de/?page_id=185

List of genome announcement, notes and reporting journals

Jit — Wed, 26 Jul 2017 08:01:38 -0500

Faced with an increasing number of articles describing DNA data and a need for more appropriate venues to present these data, some publishers and journals have responded by changing the structure and format of genome papers. Specifically, certain journals have started accepting very short manuscripts (500–1500 words) that present a new chromosome sequence, its GenBank accession number and little else. These pint-sized articles go by various names, such as genome reports, genome announcements, genome notes or genome letters, but will be referred to here broadly as genome reports. Their short length and minimal number (or complete absence) of figures, tables and article subheadings are a significant departure from long-form genome papers, which typically span 8–10 journal pages, contain many supporting items and have formal introduction, methods, results and discussion sections.

Following are the list of journals publishing pint-sized articles go by various names, such as genome reports, genome announcements, genome notes or genome letters, but will be referred to here broadly as genome reports.

1. Genome Announcements, American Society for Microbiology, Genome announcement, Impact factor 1.3, A 500-word report stating that the genome of a particular organism (prokaryote, eukaryote or virus) has been sequenced and providing a citable record of the corresponding GenBank submission. Must include abstract but no text headings can be used except for ‘Acknowledgments’ and ‘References’. Cannot include figures, tables or supplemental material to present data or analysis.

Link: https://mra.asm.org/

2. Genome Biology and Evolution, Oxford University Press, Genome report, Impact factor 4.2, Focused 1500-word papers (up to six tables or figures) that publish the main evolutionary message of new genome sequences as they become submitted to GenBank. May also contain specifically focused comparative analyses of previously published genomes that contain a substantial and novel insight of broadest evolutionary significance.

Link: https://academic.oup.com/gbe

3. Journal of Biotechnology, Elsevier, Genome announcement, Impact factor 2.9, A 500-word report announcing the availability of the completely annotated genome sequence of a biotechnologically relevant organism in the corresponding database (for eukaryotes, advanced draft genomes will also be considered). Articles can contain an Abstract, a brief report on the organism and its biotechnological relevance, a table summarizing the genome features, References and an Acknowledgement. Figures are generally not allowed.

Link: https://www.journals.elsevier.com/journal-of-biotechnology

4. Journal of Genomics, Ivyspring, Genome note, Impact factor N/A, A 1000-word report (10 reference limit; conclusions not permitted) describing novel data sets from high-throughput analysis of genotypes, phenotypes, gene expression, metabolomes, proteomes or genome assemblies.Standard metrics for data quality and the experimental design must be clearly reported.

Link: http://www.jgenomics.com/

5. Memórias do Instituto, Oswaldo Cruz Oswaldo Cruz Foundation, Genome announcement and highlight, Impact factor 1.6, Dedicated to publishing new genome information from eukaryote parasites, virus, bacteria and their respective vectors, as well as re-sequencing or comparative genome analyses. Should occupy no more than three printed pages including figures and/or tables.

Link: http://memorias.ioc.fiocruz.br/

6. Molecular Ecology Resources, Wiley, Genomic resources note, Impact factor 3.7, Short notes on newly assembled and annotated transcriptomes, genome fractions or whole genomes, and/or a library of SNP/SSR markers.Authors submit a short manuscript describing how the resource was developed and where the data can be accessed. Do not appear in journal as individual papers but are instead published as part of a summary article.

Link: https://onlinelibrary.wiley.com/journal/17550998

7. Standards in Genomic Science, BioMed Central (Springer), Short genome report, Impact factor 3.2, Short (∼500-word) article on newly sequenced genome. Article format must follow guidelines and template (available from journal Web site) put forward by the SGS. Any manuscripts not using template or that are missing key figures, tables and/or references (as per the guidelines) will be returned to authors. Rationale of the content model is to provide information that is consistently and uniformly presented for rapid and easy consumption by both human and machine readers.

Link: https://standardsingenomics.biomedcentral.com/

8. 3biotech, Springer, Short genome report, Impact factor 1.3, Short (∼500-word) article on newly sequenced genome. Article format must follow guidelines (available from journal Web site). Genome of a particular organism (prokaryote, eukaryote or virus) has been sequenced and providing a citable record of the corresponding GenBank submission.

Link: https://link.springer.com/journal/13205