<commit_before># SequenceServer (Beta 1)

Biologists constantly generate new sequence data. However, it is challenging to effectively 
share and search and compare sequence data. Deploying complex solutions such as
[GMOD][5] is often overkill, and publicly available front ends for BLAST such as 
[NCBI's wwwblast][21] are difficult to use or install. 
There is a need for an easy-to-deploy and easy-to-use solution.

SequenceServer allows rapid creation of a web page to [BLAST][1] search 
sequence databases by using an intuitive user interface. SequenceServer can 
be used as a local point and click interface to [NCBI BLAST+][2], or to 
provide one over the web. SequenceServer uses [NCBI BLAST+][2], 
[Sinatra][3], and [jQuery][4].

## Features

Ease of use for biologists:

* a single iPod-like search page
* intuitive and helpful web interface: automatic sequence type detection that helps
  choose appropriate BLAST method and database types
* links to easily download sequences of BLAST hits
* support for advanced options.
  
  
Rapid deployment for bioinformatics administrators:

* assisted formatting of BLAST databases (with sequence type detection)
* automatic discovery of formatted BLAST databases during startup
* uses ruby's internal web server (on any open port) or Apache
* add custom hyperlinks to identified hits (to your genome browser or custom database)
* open source & freely available for non-profits.


## Setup

### Requirements

The following software is required to run SequenceServer:

* [NCBI BLAST+][2]  ( at least 2.2.18 )
* [Ruby][6]         ( tested with 1.8.7 and 1.9.2)

### Download

Get the latest version SequenceServer from: https://github.com/yannickwurm/sequenceserver/archives/master.

Or download the zip in the command-line:

    wget http://github.com/yannickwurm/sequenceserver/zipball/master
 

### Installation

Unzip/Untar the downloaded file, cd to SequenceServer's directory and issue the following command that will make sure you have the required ruby dependencies:
<commit_msg>README: add output filename with .zip extension to download instructions<commit_after># SequenceServer (Beta 1)

Biologists constantly generate new sequence data. However, it is challenging to effectively 
share and search and compare sequence data. Deploying complex solutions such as
[GMOD][5] is often overkill, and publicly available front ends for BLAST such as 
[NCBI's wwwblast][21] are difficult to use or install. 
There is a need for an easy-to-deploy and easy-to-use solution.

SequenceServer allows rapid creation of a web page to [BLAST][1] search 
sequence databases by using an intuitive user interface. SequenceServer can 
be used as a local point and click interface to [NCBI BLAST+][2], or to 
provide one over the web. SequenceServer uses [NCBI BLAST+][2], 
[Sinatra][3], and [jQuery][4].

## Features

Ease of use for biologists:

* a single iPod-like search page
* intuitive and helpful web interface: automatic sequence type detection that helps
  choose appropriate BLAST method and database types
* links to easily download sequences of BLAST hits
* support for advanced options.
  
  
Rapid deployment for bioinformatics administrators:

* assisted formatting of BLAST databases (with sequence type detection)
* automatic discovery of formatted BLAST databases during startup
* uses ruby's internal web server (on any open port) or Apache
* add custom hyperlinks to identified hits (to your genome browser or custom database)
* open source & freely available for non-profits.


## Setup

### Requirements

The following software is required to run SequenceServer:

* [NCBI BLAST+][2]  ( at least 2.2.18 )
* [Ruby][6]         ( tested with 1.8.7 and 1.9.2)

### Download

Get the latest version SequenceServer from: https://github.com/yannickwurm/sequenceserver/archives/master.

Or download the zip in the command-line:

    wget http://github.com/yannickwurm/sequenceserver/zipball/master -O sequenceserver.zip
 

### Installation

Unzip/Untar the downloaded file, cd to SequenceServer's directory and issue the following command that will make sure you have the required ruby dependencies:

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