Difference between revisions of "BLAST"
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== Installed version == | == Installed version == | ||
These versions are installed and and currently available... | |||
== Using BLAST | ... on envirnoment ''hpc-uniol-env'': | ||
*'''BLAST/2.2.26''' | |||
*'''BLAST/2.6.0''' | |||
*'''BLAST+/2.7.1'''-intel-2016b-Python-2.7.12 | |||
... on environment ''hpc-env/6.4'': | |||
*'''BLAST+/2.7.1'''-intel-2018a | |||
*'''BLAST+/2.7.1'''-foss-2017b-Python-2.7.14 | |||
... on environment ''hpc-env/8.3'': | |||
*'''BLAST/2.11.0'''-Linux_x86_64 | |||
*'''BLAST+/2.11.0'''-gompi-2019b | |||
*'''BLAST+/2.13.0'''-gompi-2019b | |||
== Available Commands == | |||
BLAST offers three categories of applications: | |||
* '''search tools''': blastn, blastp, blastx, tblastx, tblastn, psiblast, rpsblast, rpstblastn | |||
* '''BLAST database tools''': makeblastdb, blastdb_aliastool, makeprofiledb, blastdbcmd | |||
* '''sequence filtering tools''': segmasker, dustmasker, windowmasker | |||
== Using BLAST == | |||
If you want to find out more about BLAST on the HPC Cluster, you can use the command | If you want to find out more about BLAST on the HPC Cluster, you can use the command | ||
| Line 15: | Line 39: | ||
This will show you basic informations e.g. a short description and the currently installed version. | This will show you basic informations e.g. a short description and the currently installed version. | ||
To load the desired module, use the command, e.g. | To load the desired version of the module, use the command, e.g. | ||
module load BLAST/2.6.0-Linux_x86_64 | module load BLAST/2.6.0-Linux_x86_64 | ||
Always remember: this command is case sensitive! | Always remember: this command is case sensitive! | ||
<!-- | |||
== Using BLAST with the HPC Cluster == | |||
--> | |||
== Documentation == | == Documentation == | ||
The full documentation can be found [http://blast.ncbi.nlm.nih.gov/ here]. | The full documentation can be found [http://blast.ncbi.nlm.nih.gov/ here]. | ||
Direct link to the command line manual (PDF viewer required): [https://www.ncbi.nlm.nih.gov/books/NBK279690/pdf/Bookshelf_NBK279690.pdf BLAST® Command Line Applications User Manual] | |||
Latest revision as of 17:14, 22 March 2022
Introduction
In bioinformatics, BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold.
Installed version
These versions are installed and and currently available...
... on envirnoment hpc-uniol-env:
- BLAST/2.2.26
- BLAST/2.6.0
- BLAST+/2.7.1-intel-2016b-Python-2.7.12
... on environment hpc-env/6.4:
- BLAST+/2.7.1-intel-2018a
- BLAST+/2.7.1-foss-2017b-Python-2.7.14
... on environment hpc-env/8.3:
- BLAST/2.11.0-Linux_x86_64
- BLAST+/2.11.0-gompi-2019b
- BLAST+/2.13.0-gompi-2019b
Available Commands
BLAST offers three categories of applications:
- search tools: blastn, blastp, blastx, tblastx, tblastn, psiblast, rpsblast, rpstblastn
- BLAST database tools: makeblastdb, blastdb_aliastool, makeprofiledb, blastdbcmd
- sequence filtering tools: segmasker, dustmasker, windowmasker
Using BLAST
If you want to find out more about BLAST on the HPC Cluster, you can use the command
module spider blast
This will show you basic informations e.g. a short description and the currently installed version.
To load the desired version of the module, use the command, e.g.
module load BLAST/2.6.0-Linux_x86_64
Always remember: this command is case sensitive!
Documentation
The full documentation can be found here.
Direct link to the command line manual (PDF viewer required): BLAST® Command Line Applications User Manual
