Genetic Engineering & Biotechnology News

JUN15 2018

Genetic Engineering & Biotechnology News (GEN) is the world's most widely read biotech publication. It provides the R&D community with critical information on the tools, technologies, and trends that drive the biotech industry.

Issue link: https://gen.epubxp.com/i/990176

Contents of this Issue

Navigation

Page 35 of 37

For more information, visit our website (GENengnews.com), click on New Products, and search through our comprehensive new products database. New Products 34 | JUNE 15, 2018 | Genetic Engineering & Biotechnology News | GENengnews.com Best of the Web All of the links to the URLs described above are posted on GEN's website, www.GENengnews.com. To suggest a website for Best of the Web, please send the URL to Taralyn Tan (ttan@GENengnews.com). Key Strong Points Weak Points Excellent Ratings Very Good Good 9 – HHHH HHH HH MORPHEUS HHHH software.broadinstitute.org/morpheus 9 Good tutorial, many sample datasets As a visualization tool for large genomic data- sets, MORPHEUS is every researcher's dream. A product of the Broad Institute in Cambridge, MA, MORPHEUS allows researchers to quickly and eas- ily visualize large data matrices as a heat map. On top of that, analysis tools allow users to perform hierarchical clustering, sort and filter the data, and further explore the dataset. Users can upload data to MORPHEUS in a variety of ways, including as an Excel file from one's computer, a URL, a text file, or a file imported from Google Drive or Dropbox. To get started, though, users can familiarize themselves with MORPHEUS using one of the many pre-loaded genomics datasets. For a given dataset, users can choose to analyze gene expression, proteomics methylation, or other specific aspects of the data. Of note, all data processing occurs locally on one's computer as opposed to on a server. COSMIC HHHH cancer.sanger.ac.uk/cosmic 9 Incredible amount of data, nicely organized site COSMIC—the Catalog of Somatic Mutations in Can- cer, from the Wellcome Sanger Institute—is an incred- ibly rich resource for cancer biologists and medical professionals. (In fact, as the website boasts, COSMIC is the "world's largest and most comprehensive resource" on somatic mutations in human cancers.) COSMIC itself is comprised of several projects. There is a curated database of somatic mutations (COSMIC), genetic information for over 1000 cancer cell lines (Cell Lines Projects), a 3D browser to analyze genetic mutations in the context of 3D protein structures (COSMIC-3D), and a catalog of causally linked oncogenes (Cancer Gene Census). The nicely organized COSMIC website includes tools for the visualization of genetic data and genomic analyses, a news feed, and a wealth of data that are all free to download. The site houses a good amount of documentation to help researchers navigate the site. LAGAN Alignment Toolkit Website HHH lagan.stanford.edu/lagan_web/index.shtml 9 Multiple alignment options, downloadable source code – Alignment results not returned in-browser (emailed) The LAGAN Alignment Toolkit consists of three online alignment tools. Pairwise-LAGAN allows users to perform global alignments of two sequences; Multi-LAGAN performs global alignment of up to 31 sequences; and Shuffle-LAGAN is a "glocal" alignment tool (yes, refer- ring to both global and local features) that can identify genomic rear- rangements such as duplications and inversions within a global align- ment framework. To use these tools, users can upload sequence files or can enter GENBANK identifiers. An email address is also required, as users are emailed a link to view their results on the VISTA server upon completion of the alignment. Re- sults are kept on the server for seven days. Users can download the alignment results as a pdf, though the VISTA server also includes its own dynamic, JAVA-based alignment-visualization tool. Site users can access instructions for the browser from the results page. Clutch HHH www.clutchprep.com 9 Good quality videos, large video collection – Few truly "free" videos, mostly requires a paid subscription Clutch is a study service for students that provides a large collection of tutorial and review videos. These videos span multiple STEM disciplines such as biochemistry, genetics, and anatomy and physiology, and they are designed to accompany specific textbooks and chapters. As such, students or educa- tors can indicate their college or university (if listed) to easily find the video resources pertaining to the textbooks used at their school. Alternatively, users can simply select from among the textbook options that are presented for a given subject. To sign up for the site users must have a school email address ending in ".edu". Somewhat annoyingly, a phone number is also required (both to receive a validation code as well as to automatically receive text messages from one's individually assigned tutor). Signing up for the website is free; however, users are only given three video "tokens" upon initial registration. To earn additional video views, users can opt to invite friends, download the app, or purchase a subscription. Animal TFDB HHH bioinfo.life.hust.edu.cn/AnimalTFDB/ 9 Sizable database, nice site design The Animal Transcription Factor DataBase (Animal TFDB) from the Guo Lab at the Huazhong University of Science and Technol- ogy is a wonderfully rich database of…well, you get the idea. Impressively, the database includes genetic information for 65 animal species. From the homepage, site visitors can quickly browse transcription factors (as well as transcription co-factors and chromatin remodeling factors) either by species or by protein family. From there, visitors can explore individual family members. A brief description of each protein family is provided, and site visitors can view information for individual members by clicking on the Ensembl or Entrez ID for each entry. Sequence alignments and phylogenetic trees are also provided for various protein families. In addition to browsing the entries, users can search the data- base by gene annotation, by mRNA expression, or by human protein expression. Roadmap Epigenomics Project HHH www.roadmapepigenomics.org/data/ 9 Large amount of data, plus experimental protocols and tools – Data and news only current as of 2015 Roadmap Epigenomics Project is the website for the NIH Road- map Epigenomics Mapping Consortium. The mission of the consortium is to make publicly available resources related to the human "epigenome," which consists of the patterns of DNA methylation, the chemical modifications to histone proteins, and the small, non-coding RNAs of the genome. In service of this goal, the website for the Roadmap Epigenomics Project includes a data browser for the epigenomic maps generated from stem cells and ex vivo tissues, a series of standardized experimental protocols, and a series of downloadable tools for genomic analyses. Site visi- tors will also find a list of the publications whose data are included in the consortium's Human Epigenome Atlas (though the most recent listings are from 2015). The vari- ous sections of the website (such as project data, publications, and protocols) are easily accessed from a menu bar that is prominently displayed on the homepage.

Articles in this issue

Links on this page

Archives of this issue

view archives of Genetic Engineering & Biotechnology News - JUN15 2018