There are many tools at NCBI, with a huge range of functions. Literature, sequence data, variations, protein structure, chemicals and bioassays, and more. It’s hard to keep track of what’s available. Their video tutorials are helping me to be aware of new tools, and new features within existing tools. For this week’s Tip of the Week, we’ll look at their recent video for ProSplign. It’s a tool that will help you align protein information to genomic sequences.
Although the Genome Workbench itself has been around for a while (we featured it as a tip it first in 2013), it is constantly underdevelopment, and new features are available regularly. And although this tip focuses on how to use the ProSplign piece, if you haven’t used it much it will help you to understand how a number of tools within the Workbench can be accessed. You can also see that Splign is available in the tool list–which is another NCBI tool for a similar type of process, but with mRNA sequences as the focus.
If you want to have a text-based type of walk-through instead, there is a page that will take you through the features (see the quick links below). And there are other videos that will help you to explore the Genome Workbench features as well–there’s a handy special playlist of just those videos. Subscribe to their YouTube channel for notices of their new items.
NCBI’s Genome Workbench: http://www.ncbi.nlm.nih.gov/tools/gbench/
Text-based tutorial page: https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial13/
Kapustin, Y., Souvorov, A., Tatusova, T., & Lipman, D. (2008). Splign: algorithms for computing spliced alignments with identification of paralogs Biology Direct, 3 (1) DOI: 10.1186/1745-6150-3-20
NCBI staff (2016). Database resources of the National Center for Biotechnology Information Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1290