BLAST search made easy!

SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.Sequence data is generated at increasing rates. However it is challenging to effectively share and query such data. Deploying complex solutions such as GMOD is often overkill and publicly available front ends for BLAST are difficult to use or install.SequenceServer is an efficient and elegant alternative. Sequenceserver is still being developed yet is fully functional and has already been deployed for multiple databases.SequenceServer is free for academics. Itssource code is available on GitHub.

Easy for biologists

• Minimalistic, clutter-free design, so you can focus on the biology
• The smart user interface automagically figures out the appropriate BLAST method to use based on your input and selected databases
• Common mistakes prevented. E.g., SequenceServer warns if you mix nucleotide and protein sequences
• Advanced users: use advanced parameters (e.g. -task blastn-short -evalue 1.0e-20) like you would in the command line.
• Simple overview of results
• Download links for hits

Rapidly deployed by admins

• very little configuration required: only a directory containing formatted or un-formatted sequence databases
• SequenceServer scans the database directory during startup. And will interactively help you create BLAST databases from FASTA files
• Comes with a built-in web server. No need to deal with Apache or Nginx to run SequenceServer.
• Easily customizable hyperlinks to search hits (e.g. to your local genome browser or custom database)

Requirements

Ruby (>= 1.8.7), RubyGems (>= 1.3.6), and NCBI BLAST+ (>= 2.2.25+). That's it!

Linux and MacOS are officially supported. While we would like to also support Windows, our resources are limited and we prefer to first concentrate on making SequenceServer great on fewer platforms.

Demo server

Sure, check Ant genome BLAST or the sites of some of our users.

Download & Setup in just a few minutes

Installation

Run the following from a command line to get the latest release of SequenceServer.

 $ gem install sequenceserver

If that doesn't work, try sudo gem instead of gem. And subsequently follow the instructions on screen.

Configuration

SequenceServer needs to know the location of the BLAST+ binaries, and the BLAST database. This is accomplished by providing a .sequenceserver.conf in the user's home directory.

# .sequenceserver.conf
bin: ~/ncbi-blast-2.2.25+/bin/
database: /Users/me/blast_databases/
      

SequenceServer automatically generates a fully commented configuration file (.sequenceserver.conf) in the user's home directory if it can't find one. Uncomment the relevant lines (i.e remove the # signs), edit the values, and run SequenceServer.

If you you already have databases, jump ahead to launch SequenceServer. If not, set up databases as follows.

Setting up BLAST databases

To set up BLAST databases from a directory of FASTA sequence files, use sequenceserver's format-databases subcommand:

$ sequenceserver format-databases

It will automatically pick up the database directory from the configuration file. Or pass the database directory from command line:

$ sequenceserver format-databases directory_with_fasta_files

The script will assist you by:

• finding FASTA files in directory_with_fasta_files (and in subdirectories too)
• detecting the sequence type of each file
• asking you to name each database
• subsequently running the appropriate makeblastdb commands.

Alternatively, manually set up BLAST databases from single FASTA sequence files. In the directory containing the FASTA file, run:

$ makeblastdb -dbtype <db type> -title <db title> -in <db> -parse_seqids

Where,

• <db type> is either prot, or nucl depending on the type of sequence
• <db title> is what users will see
• <db> is the path to the FASTA file
• -parse_seqids is required to generate links for downloading search hits (yes, it's a bit slow on large files).
• Additional options at makeblastdb -help.

Launch SequenceServer

Simply execute:

$ sequenceserver 

For more information  click  here

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