Editing CrocoBLAST:UserManual (section)

=2. Manage databases=

The first time you add a database into CrocoBLAST, it will be set as an internal entry with a given name, so that in the future it is easier for you to access this database. All databases entered in CrocoBLAST can be inspected in the “Manage databases” tab.

==2.1. Retrieving and adding a database from the NCBI servers==
In the most typical scenario, you will use the established [https://ftp.ncbi.nlm.nih.gov/blast/documents/blastdb.html reference sequence databases maintained by NCBI]. CrocoBLAST allows you to specify the name of such a database, and will download or update the database for you:

{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" width="650px"
 |- 
 |<!--Col1-->'''a)''' Select the “Manage databases” tab.
 |<!--Col2-->'''b)''' Select “Download from NCBI” as a source for the database
 |-
 |<!--Col1-->[[File:CrocoBLAST AddNCBIdatabase1.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST AddNCBIdatabase2.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''c)''' Select the type of database that you want to add
 |<!--Col2-->'''d)''' Select the name of database that you want to add
 |-
 |<!--Col1-->[[File:CrocoBLAST AddNCBIdatabase3.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST AddNCBIdatabase4.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''e)''' Choose the output folder in which the database will be set up
 |<!--Col2-->'''f)''' Click the “Download and add database” button (note the log message below) 
 |-
 |<!--Col1-->[[File:CrocoBLAST AddNCBIdatabase5.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST AddNCBIdatabase6.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''g)''' The log may get messy but do not worry. All you need is the success message!
 |-
 |<!--Col1-->[[File:CrocoBLAST AddNCBIdatabase7.png|800x800px]]
 |}

==2.2. Adding a pre-formatted database from your computer==
If you have already downloaded the databases from NCBI, or if you do not have internet connection, you may add to the CrocoBLAST index database files stored on your computer. The following command can be used when you have pre-formatted database files (e.g., psq or nsq): 

{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" width="650px"
 |- 
 |<!--Col1-->'''a)''' Select the “Manage databases” tab.
 |<!--Col2-->'''b)''' Select “From formatted BLAST database files” as a source for the database
 |-
 |<!--Col1-->[[File:CrocoBLAST AddFORMATTEDdatabase1.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST AddFORMATTEDdatabase2.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''c)''' Select the type of database that you want to add
 |<!--Col2-->'''d)''' Choose the formatted database file containing the desired database
 |-
 |<!--Col1-->[[File:CrocoBLAST AddFORMATTEDdatabase3.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST AddFORMATTEDdatabase4.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''e)''' Click the “Add formatted database” button (note the log message below). That is all!
 |-
 |<!--Col1-->[[File:CrocoBLAST AddFORMATTEDdatabase5.png|800x800px]]
 |}
 
Note that CrocoBLAST will assume that all database files related to the given ".nsq" file are contained in the same folder (which is most likely the case).

== 2.3. Adding  a database from a FASTA/FASTQ sequence file in your computer ==
If you have already downloaded the databases from NCBI, or if you do not have internet connection, you may add to the CrocoBLAST index database files stored on your computer. Remember to provide a unique and representative name for each database you add, so that it is easy to refer to the databases later. When your database is in FASTA or FASTQ format, you will need to tell CrocoBLAST the '''type of sequence''' it will find in the file:

{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" width="650px"
 |- 
 |<!--Col1-->'''a)''' Select the “Manage databases” tab.
 |<!--Col2-->'''b)''' Select “From FASTA/FASTQ file” as a source for the database
 |-
 |<!--Col1-->[[File:CrocoBLAST AddSEQdatabase1.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST AddSEQdatabase2.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''c)''' Select the type of database that you want to add
 |<!--Col2-->'''d)''' Choose the sequence file to be converted into a BLAST database
 |-
 |<!--Col1-->[[File:CrocoBLAST AddSEQdatabase3.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST AddSEQdatabase4.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''e)''' Change the database name if you want (it uses the file name as default)
 |<!--Col2-->'''f)''' Choose the output folder in which the database will be set up
 |-
 |<!--Col1-->[[File:CrocoBLAST AddSEQdatabase5.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST AddSEQdatabase6.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''g)''' Click the “Add database from sequence” button (note the log message below). That is all!
 |-
 |<!--Col1-->[[File:CrocoBLAST AddSEQdatabase7.png|800x800px]]
 |}

Formatted BLAST database files will be generated in the specified output folder.

== 2.4 Removing a database ==
In case there is a missing entry in a database set for CrocoBLAST, or you have a new version of some database which name is already in use, it might be useful to remove a database from CrocoBLAST. However, you should not that this action will not delete the database files, but only remove them from CrocoBLAST managing system. For deleting the database files (which can save you a significant amount of hard disk space), you should check its location and manually delete the corresponding database files.

{| class="wikitable" border="1" style="margin: 1em auto 1em auto;" width="650px"
 |- 
 |<!--Col1-->'''a)''' Select the database you wish to remove.
 |<!--Col2-->'''b)''' Click the “Remove selected DB” button.
 |-
 |<!--Col1-->[[File:CrocoBLAST RemoveDB1.png|800x800px]]
 |<!--Col2-->[[File:CrocoBLAST RemoveDB2.png|800x800px]]
 |- style="background: #313131;"
 |
 |
 |-
 |<!--Col1-->'''c)''' Verify that the database list has been updated. That is all!
 |-
 |<!--Col1-->[[File:CrocoBLAST RemoveDB3.png|800x800px]]
 |}

In case you accidentally removed a database by mistake, do not worry: as CrocoBLAST does not automatically delete the database files, you can re-add your database to CrocoBLAST with the commands in example 2.2.