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nucleotide -> nucleic-acid and adds code blocks
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averissimo committed Oct 5, 2017
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40 changes: 22 additions & 18 deletions README.md
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Expand Up @@ -41,13 +41,13 @@ BLAST+ (pre-requirement)| [v2.2.30 (32-bit)](ftp://ftp.ncbi.nlm.nih.gov/blast/ex
### How to use MassBlast?

- Place fasta files with queries at `db_and_queries/queries` folder.
- You can have as many files as needed, see below for an example of a nucleotide query
- You can have as many files as needed, see below for an example of a nucleic-acid query
- 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, check `user.yml.example` for more information.
- run mass-blast script *(either double click it on Windows or as a command in the command line.*

Example of a nucleotide query file that could be placed in `db_and_queries/queries` folder:
Example of a nucleic-acid query file that could be placed in `db_and_queries/queries` folder:

```
>Example01
Expand Down Expand Up @@ -128,41 +128,45 @@ Using makeblastdb command that comes bundled with Blast+
- Go to directory that has the fasta file with the assembly
- Run makeblastdb command in that directory

- nucleotides database
- nucleic-acids database

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

- protein database
- protein database

$ makeblastdb -in &lt;filename&gt; -dbtype nucl -out "&lt;blast_db_new_name&gt;" -title "&lt;blast_db_new_name&gt;"
`$ makeblastdb -in <filename> -dbtype nucl -out "<blast_db_new_name>" -title "<blast_db_new_name>"`

*note:* do to not use spaces in the &lt;blast db new name&gt;

#### Quickly setup databases

Place the fasta files for the database in db_and_queries/import_dbs directory and run the appropriate script.

You also need to say if it is a nucleotide or protein-based fasta file.
You also need to say if it is a nucleic-acid or protein-based fasta file.

For Linux and Mac OS X run the `import_fastas.sh` script

$ cd db_and_queries/import_dbs
# for nucleotide
$ sh import_fastas.sh nucl
# for protein
$ sh import_fastas.sh prot
```
$ cd db_and_queries/import_dbs
# for nucleic-acid
$ sh import_fastas.sh nucl
# for protein
$ sh import_fastas.sh prot
```

For Windows run the `import_fastas.bat` script

$ cd db_and_queries/import_dbs
# for nucleotide
$ import_fastas.bat nucl
# for protein
$ import_fastas.bat prot
```
$ cd db_and_queries/import_dbs
# for nucleic-acid
$ import_fastas.bat nucl
# for protein
$ import_fastas.bat prot
```

### Related Tools

- [ORF-Finder](http://github.com/averissimo/orf_finder): Finds the longest Open Reading Frame from a nucleotide sequence
- [ORF-Finder](http://github.com/averissimo/orf_finder): Finds the longest Open Reading Frame from a nucleic-acid sequence
- [BioRuby](http://bioruby.org/): Open source bioinformatics library for Ruby
- [Gene Extractor](https://github.com/averissimo/gene-extractor/): can be used to extract genes from Kegg2 and GenBank using keyword search
- [MassBlast package bundler](https://github.com/averissimo/app-mass-blast): Creates a package that can be easily used in all main Operating Systems without having to install Ruby and any Ruby dependecies
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36 changes: 18 additions & 18 deletions docs/index.md
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Expand Up @@ -37,13 +37,13 @@ BLAST+ (pre-requirement)| [v2.2.30 (32-bit)](ftp://ftp.ncbi.nlm.nih.gov/blast/ex
### How to use MassBlast?

- Place fasta files with queries at `db_and_queries/queries` folder.
- You can have as many files as needed, see below for an example of a nucleotide query
- You can have as many files as needed, see below for an example of a nucleic-acid query
- 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, check `user.yml.example` for more information.
- run mass-blast script *(either double click it on Windows or as a command in the command line.*

Example of a nucleotide query file that could be placed in `db_and_queries/queries` folder:
Example of a nucleic-acid query file that could be placed in `db_and_queries/queries` folder:

```
>Example01
Expand Down Expand Up @@ -74,45 +74,45 @@ Using makeblastdb command that comes bundled with Blast+
- Go to directory that has the fasta file with the assembly
- Run makeblastdb command in that directory

- nucleotides database
- nucleic-acid database

`$ makeblastdb -in &lt;filename&gt; -dbtype nucl -out "&lt;blast_db_new_name&gt;" -title "&lt;blast_db_new_name&gt;"`
`$ makeblastdb -in <filename> -dbtype nucl -out "<blast_db_new_name>" -title "<blast_db_new_name>"`

- protein database

`$ makeblastdb -in &lt;filename&gt; -dbtype nucl -out "&lt;blast_db_new_name&gt;" -title "&lt;blast_db_new_name&gt;"`
`$ makeblastdb -in <filename> -dbtype nucl -out "<blast_db_new_name>" -title "<blast_db_new_name>"`

*note:* do to not use spaces in the &lt;blast db new name&gt;

#### Quickly setup databases

Place the fasta files for the database in db_and_queries/import_dbs directory and run the appropriate script.
Place the fasta files for the database in `db_and_queries/import_dbs` directory and run the appropriate script.

You also need to say if it is a nucleotide or protein-based fasta file.
You also need to say if it is a nucleic-acid or protein-based fasta file.

For Linux and Mac OS X run the `import_fastas.sh` script

```
$ cd db_and_queries/import_dbs
# for nucleotide
$ sh import_fastas.sh nucl
# for protein
$ sh import_fastas.sh prot
$ cd db_and_queries/import_dbs
# for nucleic-acid
$ sh import_fastas.sh nucl
# for protein
$ sh import_fastas.sh prot
```

For Windows run the `import_fastas.bat` script

```
$ cd db_and_queries/import_dbs
# for nucleotide
$ import_fastas.bat nucl
# for protein
$ import_fastas.bat prot
$ cd db_and_queries/import_dbs
# for nucleic-acid
$ import_fastas.bat nucl
# for protein
$ import_fastas.bat prot
```

### Related Tools

- [ORF-Finder](http://github.com/averissimo/orf_finder): Finds the longest Open Reading Frame from a nucleotide sequence
- [ORF-Finder](http://github.com/averissimo/orf_finder): Finds the longest Open Reading Frame from a nucleic-acid sequence
- [BioRuby](http://bioruby.org/): Open source bioinformatics library for Ruby
- [Gene Extractor](https://github.com/averissimo/gene-extractor/): can be used to extract genes from Kegg2 and GenBank using keyword search
- [MassBlast package bundler](https://github.com/averissimo/app-mass-blast): Creates a package that can be easily used in all main Operating Systems without having to install Ruby and any Ruby dependecies
Expand Down

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