MarpoDB - Help

The first page the user is presented to is the Home page. Here in the search bar, keywords can be used to identify genes of interest. Keywords can be GO terms, protein names, protein families, MarpoDB IDs. Also, in this page, the user can log in, register and go to useful information pages such as the About and Help page. At the top left, a sliding sidebar can be triggered, which presents information regarding geographical locations of users, Top favoured genes and the user's saved genes. Also, a link is provided to the BLAST to MarpoDB page.

After a query has been submitted, a table with Results is presented. The table shows different hits which can be clicked to show more information the source database and the quality of the hit. Clicking on a link will present details for that gene.

The Details page presents a gene model view of the sequence referenced. Features of the gene are coloured in different colours and the user can click on them to highlight the corresponding sequence in the sequence viewer below. If logged in, a star will appear next to the gene name which can be clicked to save the gene to the users account. If the gene is also present in the Phytozome dataset for the M polymorpha Tak-1 genome, a link will be provided below the gene name. Below the sequence viewer, detailed information about the annotations for that CDS are presented in tabs. Clicking on a tab reveals InterPro annotations, BLASTp and mRNA BLAST hits if available. The sequence viewer also provides functions for copying the selected sequence, exporting the annotated GenBank file, BLASTing to NCBI and recoding the sequence to the common syntax standard for type IIS cloning.

The Recode page shows the sequence selected to be recoded with BsaI and SapI restriction sites highlighted if present. Below the sequence viewer, a selector field allows choosing of the type of fusion to be recoded to, if a CDS has been selected. Types of fusions allowed are N-terminal, C-terminal and no fusion. Once the recode button is pressed, the sequence is recoded, BsaI and SapI sites are recoded onto silent mutations (if a CDS is being recoded), and the sequence viewer is refreshed showing the new sequence with flanking BsaI sites, overhangs and old restriction sites highlighted in different colours. Presing on the export to GenBank button will download an annotated GenBank file for the recoded sequence.

If you have any doubts or comments, please e-mail Bernardo Pollak - bp358[at]cam[dot]ac[dot]uk or Mihails Delmans - md656[at]cam[dot]ac[dot]uk. Happy hunting!