5 articles Site Functions

The section explains the functionalities that are provided in ggKbase, such as search, blast, and multiple sequence alignment program.

Search

ggKbase provides several ways to find information in the system. There are two search boxes on the top grey banner that appear throughout the site. In addition to that, you can click on the Advanced Search to conduct more fine-tuned searches using Boolean logic as well as setting the scope by projects. Find by Name…

BLAST

ggKbase provides a BLAST (Basic Local Alignment Search Tool) program for sequence comparison. However, this tool is only accessible after you have signed into your account. BLAST Form The input sequence type can be genes DNA, genes protein, or contigs DNA. BLAST Flow Task Once you click on the green “Run Blast” button, you will…

Multiple Sequence Alignment Programs

You have access to two¬†multiple sequence alignment programs in your lists: MAFFT and ClustalW. You can apply it to your lists. Note: If you have a list with many contigs, these programs may take along time to finish. After you have selected a list, you will see the “Analyze list” dropdown menu. MAFFT MAFFT is…

Data Download

You may want to download data and visualizations from ggKbase for the following purposes. Store data locally on your computer Analyze data using other¬†analysis programs Share data with colleagues There are a number of ways that you can download data from ggKbase. **If you want to download data for many organisms or projects at once,…

HMM Import

HMM (Hidden Markov Model) will be incorporated into the feature/gene annotations and the lists system in ggKbase, so that ggKbase can create a genome summary with HMMs. The process of importing HMM annotations include the following. 1. Users run their HMMs using tools like hmmsearch outside of ggKbase. 2. Generate a HMM output file in…