Bioinformatic Resources

A database is a structured collection of records stored in a computer system. Genomic databases typically store DNA or protein sequences as well as annotated information about those sequences. Many databases also provide bioinformatics tools tools, such as Blast, for finding specific sequences or annotations. There are hundreds of genomics databases: some are comprehensive, but are not carefully curated (GenBank), while others are carefully curated, but are narrow (FlyBase).

Bioinformatic tools are computer programs that analyze one or more sequences. There are a dizzying array of bioinformatic tools that can analyze sequences to find protein domains (Pfam), or that can search through databases of millions of sequences to find ones that are similar (Blast) or that can find potential protein-coding regions (ORF-Finder). Many are freely available over the web. It can be overwhelming to find and use bioinformatic tools because you need to know 1) what type of analysis you wnat performed 2) what type of tool to use 3) where to find the tool.

For this class, we have made a collection of common databases and tools that should be useful for your research. But you should also feel free to use Google to try and find other databases and tools. If you want information on a particular species, you can search for databases that contain DNA sequences for that species (try Aiptasia EST database). If you want to identify possible functional domains contained within a set of sequences, you can search for annotation tools.

Bioinformatics Training

To get some training on how to use some of these tools, try working through this set of exercises (Microsoft Word 94kB Apr4 13).

Show Are you confused or overwhelmed? Familiarize yourself with the "culture" of bioinformatics

Approaching the challenge of doing bioinformatic research is daunting; there are many different bioinformatic tools, it is often difficult to figure out exactly what each one does, none of the web interfaces are the same, and the number of options that you can set are overwhelming. You may ask why it needs to be so confusing?
Consider:

Most bioinformatic tools were created by researchers to do the job, not be easy for others to use:The majority of bioinformatic tools were not designed by companies trying to make the tools easy for consumers; rather they have been designed and written by researchers in labs all over the world for use in their own research. Their focus was on creating a good bioinformatic tool that would help them address their own research questions, not really to make them intuitive for others to use.

Few standards have been adopted:The world of bioinformatics and genomics is still rapidly evolving and the community of researchers has not settled on many standard ways of organizing data or bioinformatics interfaces. This is good because it allows for innovation. But it is difficult to start out as a genomicist, because you must acclimate yourself to a culture of having to just figure stuff out as you go along.

Most researchers adhere to an open source policy:Most researchers and bioinformatics organizations (NCBI, EMBL) believe in an open sourcepolicy, in which they freely make tools available to others, usually via their websites. For example, AiptasiaBase is a newly created public website that was developed here at Vassar, in collaboration with labs at UCMerced, Stanford, and University of Oregon. But since it is new, it is not terribly intuitive to use. You will be using AiptasiaBase a lot, and you will soon get used to navigating it!

Tools/Databases evolve:Because it is such a rapidly developing field, the labs creating the tools and databases are constantly updating, creating new versions, and changing their tools and websites. You may visit a familiar bioinformatics website only to find that it has changed. This happens even with NCBI; recently they completely altered their blast interface.

There are many redundant tools:Because it is such a new field, many different people have created bioinformatic tools and databases that do very similar things. For example, Pfam and SMART are both databases of conserved protein domains, but they look very different. Check out this one website that lists dozens of tools, all for analyzing protein sequences EXPASY tools

HOW YOU CAN DEAL WITH THESE ISSUES:

The proliferation of open source bioinformatics is wonderful because everyone has access to sequence data and tools to analyze it (for example, see just one list of tools at . But it is challenging because every site has a different interface. Some sites are not intuitive to use. The best mentality for you to develop is a "spend time exploring, reading, and trying" mentality.

Rules for visiting bioinformatics websites:

Try to generally determine the purpose of the database/tool (if the group has published a paper to publicize the tool, they will post it on their website; read their paper)
Find the help page and read through it
Find the "Sequence Submission" page, and read through it.
PLAY AROUND and try things out. It may take several attempts to get it right.

Sequence Databases (with some annotation tools):

Transcriptome datasets

Aiptasia Sequences

SymBioSys is a database of transcriptome sequences for corals and Symbiodinium hosted by the Medina Lab.

Coral Transcriptome Datasets are available through the Matz Lab website.

Whole Genome Data

: JGI's Nematostella Genome Browser is a database of the genome sequence and annotations for Nematostella vectensis, a non-symbiotic sea anemone (Putnam et al., Science 2007).

Acropora digitifera Genome Browser is a web interface with access to whole-genome sequences for the first coral to have its genome published (Shinzato et al., Nature2011)

: JGI's Monosiga brevicollis Genome Browseris a database of the genome sequence and annotations for a choanoflagellate, which are one of the closest unicellular relatives of animals and provide important insights into the evolution of animals.

NCBI

: NCBI houses sets of databases of sequences for everything under the sun, including a site for designing primers

Annotation tools:

: Pfam is a database of evolutionarily conserved protein families, and annotations about the functions of those families.

: KAAS (KEGG Automatic Annotation Server) provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database and mapping them onto known biochemical/metabolic pathways.

Alignment,Phylogeny, and Evolutionary Analysis Tools:

Puzzled?
Not sure how to get started doing blast searches? Click here for help
BLAST : Blast (basic local alignment search tools)searches through large databases of sequences to identify any that are similar to a query sequence. It combines an alignment function with a search function. Almost any sequence database that you visit (including AiptasiaBase) will offer a BLAST as a way to search for sequences in that database.

Muscle Muscle will align multiple DNA or protein sequences. It is available over many different sites, in this case we are providing a link to EMBL's server.

: MEGA is a program for constructing alignments and constructing phylogenetic trees. Important:this software does NOT run from the web. You must download it onto a PC and run it locally. The SciVis computers have this software installed on them.

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Bioinformatic Resources

Bioinformatics Training

HOW YOU CAN DEAL WITH THESE ISSUES:

Sequence Databases (with some annotation tools):

Transcriptome datasets

Whole Genome Data

NCBI

Annotation tools:

Alignment,Phylogeny, and Evolutionary Analysis Tools:

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