Quick Tour to INtegrated Data warehouse of mIcrobial GenOmes (INDIGO)

We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea.

Following are how-to uses of INDIGO Features:


Search

INDIGO search engine operates across many data fields giving you the highest chance of getting a result. Just type your search words in the box.

You can search by:

Search supports AND, OR, NOT and wildcard*. You can access Search from the home page or use QuickSearch, located top right on every page.

Figure 1: Using Search option in INDIGO.

Facets

Facets show you the different places where your search words were found (eg. within Gene, Protein, Go Term, Template, etc). You can use the facets to filter for the type of results that are most important to you. When you've filtered by facets, you can even save the results straight to a List.

Figure 2: Using Facets in INDIGO.

Lists

The Lists area lets you operate on whole sets of data at once. You can upload your own Lists (e.g. favourite Genes) or save them from results tables. We also create useful Public Lists for everyone to use. Explore your data on the List Analysis Page

Here are just some of the things you can do:

You can work with Lists from the Home page or select Lists from the Tab bar, located at the top of every page.

Figure 3: Creating lists.

Templates

INDIGO predefined template searches are designed around the common tasks performed by Biologist Community. Templates provide you with a simple form that lets you define your starting point and optional filters to help focus your search.

Templates cover common questions like:

You can work with Templates from the Home page or select Templates from the Tab bar, located at the top of every page.

Figure 4: Using templates.

QueryBuilder

QueryBuilder (QB) is the backbone of INDIGO.

Its advanced interface lets you:

The easiest way to get started with QB is by editing one of INDIGO pre-existing Template searches.

You can access QueryBuilder from the Tab bar, located at the top of every page.

Figure 5: Using query builder.

BLAST interface

Basic Local Alignment Search Tool or BLAST interface allows user-defined comparison of DNA or Protein sequences to INDIGO genes. It helps to find out e.g. are there any genes in INDIGO similar to your favorite gene or gene of interest?

The BLAST result page shows the ranked list of genes and their alignments based on your search criteria. INDIGO genes in the BLAST result table are hyper-linked to view their report pages. All genes from the BLAST result table can be selected to create a list for further analysis.

Figure 6: Performing blast.
Figure 7: Viewing blast results.

MyMine

MyMine is your private space on INDIGO. Creating an account is very easy. Just provide an e-mail and a password. You're ready to go.

Your account allows you to:

You can access mMyMine from the Tab bar, located at the top of every page.

Note: Your data and e-mail address are confidential and we won't send you unsolicited mail.

Figure 8: Using private space.

Annotation pipeline; Automatic Annotation of Microbial Genomes (AAMG) for INDIGO


INDIGO interface allows submition of microbial genome annotation jobs to INDIGO's annotation engine, acronym AAMG. Only registered users are allowed to submit annotation jobs.
A link is provided to AAMG under myMine. Once logged in, Follow AAMG link to submit a microbial genome for annotation. More details on the annotation process, example AAMG annotated genomes etc. are explained in the INDIGO paper and supplementary materials available here.

Porting annotation results into INDIGO

A user need to request by sending an email to us if one needs to have their annotation results available via the INDIGO interface.

How to cite:

INDIGO - Reference

Alam I, Antunes A, Kamau AA, Wali, WB, Kalkatawi M, Stingl U, Bajic VB (2013) INDIGO – INtegrated Data warehouse of mIcrobial GenOmes with examples from the Red Sea extremophiles. PLOS ONE (2013), link


Individual Genome References:

Antunes A, Alam I, Bajic VB, Stingl U (2011) Genome sequence of Salinisphaera shabanensis, a gammaproteobacterium from the harsh, variable environment of the brine-seawater interface of the Shaban Deep in the Red Sea. J Bacteriol 193: 4555-4556.

Antunes A, Alam I, El Dorry H, Siam R, Robertson A, et al. (2011) Genome sequence of Haloplasma contractile, an unusual contractile bacterium from a deep-sea anoxic brine lake. J Bacteriol 193: 4551-4552.

Antunes A, Alam I, Bajic VB, Stingl U (2011) Genome sequence of Halorhabdus tiamatea, the first archaeon isolated from a deep-sea anoxic brine lake. J Bacteriol 193: 4553-4554.