MassBLAST

Library to query multiple files against many databases

We recommend using a packaged release of MassBlast available at this link. The only requirement is to have BLAST+ installed. See all the information in the section below.

Install and usage (from a release)

Pre-packaged releases of MassBlast are available at github, download here and support:

• Linux 32/64-bit
• Mac OSX (recent versions)
• Windowns (the binaries are 32-bits, due to our packaging tool that includes ruby and other dependencies)

Requirements:

• BLAST+ installed
  • link to download latest version
  • note for Windows users:
    1. Can only install 32-bit version of BLSAT+ (latest win32 version is 2.2.30 that can be downloaded here)
    2. If it gives an error, please delete ncbi.ini located at a subdirectory at the AppData folder, if problem persists, submit an issue.

Default options can be changed at user.yml, check user.yml.example for more information (manual soon).

How to use it?

• Place fasta files with queries at db_and_queries/queries folder.
• Place blast databases at db_and_queries/db folder.
  • Check "How to setup a Blast database for a transcriptome" below for more information on creating a Blast database.
• Edit user.yml file to change options and BLAST engine to be used.
• run mass-blast script (either double click it on Windows or as a command in the command line.

Install and usage (from source code)

We do not recommend installing from source unless you plan to develop MassBlast further. The package available already has all dependencies pre-packaged and is ready to be used.

Requirements:

• Ruby interpreter

• Bundler gem

• rub bundle install at root directory

• Options are configurable via config/user.yml file

  • Change 'db_parent' and 'query_parent' to specify the parent directories for blast databases and queries
  • Change 'dbs' and 'folder_queries' to specify the databases that should be used and which query folders should be crawled

  $ ruby script.rb

External data

The test blast database and the taxonomy database are not kept in the git tree anymore, to get this auxiliary data run the command below or call mass-blast via script.rb

$ rake bootstrap.rb

If you need to include it on your code use:

require_relative 'src/download'

ExternalData.download(path_to_db_parent)

How to test it

$  rake spec

Type of blast implemented

• Blastn
• TBlastn
• TBlastx

Methods available

All different types have two implemented methods, blast and blast_folders

• blast(qfile, db, out_file, query_parent=nil, db_parent=nil)
  • qfile: query file path - string
  • db: database name - string
  • out_file: output file path (can be relative) -string
  • query_parent: parent directory of query (optional) - string
  • db_parent: parent directory of database (optional) - string

notes: 'qfile' and 'db' arguments can be relative to 'query_parent' and 'db_parent' (respectively).

• blast_folders( folders=nil, query_parent=nil, db_parent=nil )
  • folders: list of folders (optional) - array of strings
  • query_parent: parent directory of folders (optional) - string
  • db_parent: parent directory of database (optional) - string

notes: 'folder' argument can be relative to 'query_parent'. All optional parameters must be set in the config.yml file

How to setup a Blast database for a transcriptome

Using makeblastdb command that comes bundled with Blast+

• Open the command line in your operating system

• Navigate to directory

• Go to directory that has the fasta file with the assembly

• Run makeblastdb command in that directory

  • nucleotides database

    $ makeblastdb -in <filename> -dbtype nucl -out "<blast_db_new_name>" -title "<blast_db_new_name>"

  • protein database

    $ makeblastdb -in <filename> -dbtype nucl -out "<blast_db_new_name>" -title "<blast_db_new_name>"

note: do to not use spaces in the <blast db new name>

Quickly setup databases in Linux and Mac OSX

In Linux and OSX you can place the fasta files in db_and_queries/import_dbs directory and run the import_fastas.sh script

$ cd db_and_queries/import_dbs
$ sh import_fastas.sh [nucl|prot]

In Windows run the import_fastas.bat script

$ cd db_and_queries/import_dbs
$ import_fastas.bat [nucl|prot]

Relation with other tools

• Gene Extractor: can be used to extract genes from Kegg2 and GenBank using keyword search.
• ORF-Finder: Finds the longest Open Reading Frame from a nucleotide sequence.
• MassBlast package bundler: Creates a package that can be easily used in all main Operating Systems without having to install Ruby and any Ruby dependecies.

Ackowledgements

This tool was created as a part of FCT grant SFRH/BD/97415/2013 and European Commission research project BacHBerry (FP7- 613793)

Developer