Perform a friendly BLAST search

The option 1 will perform a BLAST search using NCBI-BLAST+.

After select the option 1 you will need provide the informations bellow

1.1 You will be asked to choose between BLASTn or BLASTx (Others BLAST+ tools are not available at this moment)

1.2 Type the name of .FASTA file you want to use in the BLAST search (example: M.musculus_NCBI_entire_genome.fasta). Here is your query sequences.

1.3 You will decide to format a BLAST database or to use an already formatted (see NCBI BLAST+ documentation to more details).

1.3.1 [Format a BLAST database] Enter the name of .FASTA file that you want to format.

Example:

Mus_musculus_uniprot_swisprot.fasta

1.3.1.1 The software will run the following command to format BLAST database:

IF YOU DECIDE TO USE BLASTx

makeblastdb -in name_of_your_database_to_BLAST.fasta -dbtype prot

IF YOU DECIDE TO USE BLASTn

makeblastdb -in name_of_your_database_to_BLAST.fasta -dbtype nucl

NOTE: This command will be performed automatically and depends of your choice in item 1.1

1.3.2 To use a DATABASE already formatted] Enter the name of .FASTA file you want to use as BLAST pre formatted database. This command is useful if you already performed makeblastdb command and do not want run it again.

1.4 Enter the expected value (E-value) that you want to use in the BLAST search. Example:

1e-20

1.5 Enter how many CPU-cores you want to use in the BLAST search.

NOTE: In the linux Mint/Ubuntu environment the command nproc shows the total number of threads available in the machine

Example:

12

1.6 Enter the format of BLAST results output file you want to be generated. Here you can type help to get all available formats, or you can read the BLAST+ documentation to get more help.

Example: type 6 to generate a file in tabular format or 5 to generate a XML format

6

1.7 In this phase you can insert additional BLAST parameters separated by spaces and starting with dashes, or you can just hit ENTER key to skip

Example:

-max_target_seqs 1 -num_descriptions 10

1.8 Some BLAST parameters are mandatory to use these tools, they are:

-query			Your .FASTA file

-db 			The database to BLAST

-e-value 		The expected value of BLAST search

-num_threads 	The number of CPU cores to parallel processing of BLAST search

-outfmt			The output format of BLAST results

NOTE: You can add other BLAST parameters (see topic 1.7 of this section) After this phase you are ready, just wait and the BLAST results will be generated in the same folder that you are working. This can take a long time and depends of the size of your datasets (query.fasta and database) and the "power" of you machine.

The file will be named as follows:

BLAST-evalue.outfmt