<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/31377?offset=1640 https://bioinformaticsonline.com/researchlabs/view/5310/bergman-lab Thu, 03 Oct 2013 17:20:09 -0500 <![CDATA[Bergman Lab]]> Broad area of research:

Genome Annotation and Functional Genomics

Bergman Lab is actively engaged in the development and application of computational methods to improve the annotation of functional biological features in genome sequences. Bergman Lab work focuses on improving annotation of non-protein-coding regions of the genome including conserved noncoding sequences (CNSs), cis-regulatory modules (CRMs), transcription factor binding sites (TFBSs), transposable elements (TEs) and noncoding RNA (ncRNA) genes. Current projects include improving the (i) annotation of TEs in the fly and yeast genomes, (ii) annotation of CRMs and TFBSs in the fly genome, and (iii) analysis of transposon knockout collections in flies. Research in this area is supported by the EC FP7 programme.

Genome and Molecular Evolution
Text and Data Mining

More @ http://bergmanlab.smith.man.ac.uk/

]]> https://bioinformaticsonline.com/bookmarks/view/39450/apollo-first-instantaneous-collaborative-genomic-annotation-editor-available-on-the-web Fri, 31 May 2019 19:55:39 -0500 https://bioinformaticsonline.com/bookmarks/view/39450/apollo-first-instantaneous-collaborative-genomic-annotation-editor-available-on-the-web <![CDATA[Apollo: First instantaneous, collaborative genomic annotation editor available on the Web]]>
  • Apollo is a plug-in for the JBrowse Genome Viewer.
  • In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transposable elements; each annotation type has its own configuration of the ‘Information Editor’.
  • History tracking with undo/redo functions is available.
  • Users are able to directly set an annotation to a specific state, choosing from the ‘History’ display.
  • Adding and updating PubMed IDs will prompt users with a publication title to confirm their submission.
  • Gene Ontology (GO) terms are supported and GO ID auto-completion has been incorporated.
  • Users may access a ‘Recent Changes’ page.
  • Help page with Apollo specific content is available.

    • Address of the bookmark: http://genomearchitect.github.io/

    ]]>     Jit     https://bioinformaticsonline.com/news/view/5436/the-anatomy-of-successful-computational-biology-software Thu, 10 Oct 2013 11:53:08 -0500 https://bioinformaticsonline.com/news/view/5436/the-anatomy-of-successful-computational-biology-software <![CDATA[The anatomy of successful computational biology software]]> Creators of software widely used in computational biology discuss the factors that contributed to their success

    Nature Biotechnology spoke with Altschul and several other originators of computational biology software programs widely used today (Table 1). The conversations explored what makes certain software tools successful, the unique challenges of developing them for biological research and how the field of computational biology, as a whole, can move research agendas forward. What follows is an edited compilation of interviews.

    Detail @ http://www.nature.com/nbt/journal/v31/n10/full/nbt.2721.html

    News Source @ Nature

    ]]>     Jitendra Narayan     https://bioinformaticsonline.com/bookmarks/view/40302/simug-a-general-purpose-genome-simulator Thu, 28 Nov 2019 04:33:18 -0600 https://bioinformaticsonline.com/bookmarks/view/40302/simug-a-general-purpose-genome-simulator <![CDATA[simuG: a general-purpose genome simulator]]> Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a lightweight tool for simulating the full-spectrum of genomic variants (single nucleotide polymorphisms, Insertions/Deletions, copy number variants, inversions and translocations) for any organisms (including human). The simplicity and versatility of simuG make it a unique general-purpose genome simulator for a wide-range of simulation-based applications.

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

    ]]>     BioStar