rBLAST | Interface for the Basic Local Alignment Search Tool | Genomics library

by mhahsler R Version: Current License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | rBLAST Summary

rBLAST is a R library typically used in Artificial Intelligence, Genomics applications. rBLAST has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases with the Bioconductor infrastructure. This includes interfaces to blastn, blastp, blastx, and makeblastdb. The BLAST software needs to be downloaded and installed separately.

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Quality

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Support

rBLAST has a low active ecosystem.

It has 55 star(s) with 17 fork(s). There are 1 watchers for this library.

It had no major release in the last 6 months.

There are 4 open issues and 12 have been closed. On average issues are closed in 131 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of rBLAST is current.

Quality

rBLAST has 0 bugs and 0 code smells.

Security

rBLAST has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

rBLAST code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

rBLAST is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

rBLAST releases are not available. You will need to build from source code and install.

Installation instructions, examples and code snippets are available.

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rBLAST Key Features

No Key Features are available at this moment for rBLAST.

rBLAST Examples and Code Snippets

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Community Discussions

Trending Discussions on rBLAST

How to run blastp in rblast?

QUESTION

How to run blastp in rblast?

Asked 2021-Oct-02 at 18:57

I'm trying to use rBlast for protein sequences but somehow it doesn't work. It works fine for nucleotide sequences but for proteins it just doesn't return any match (I used a sequence from the searched dataset, so there can't be no match). In the description it stands "This includes interfaces to blastn, blastp, blastx..." but in the help file in R studio it says "Description Execute blastn from blast+". Did anybody run rBlast for proteins?

Here's what I ran:

...

ANSWER

Answered 2021-Sep-30 at 06:10

Tried to reproduce the error but everything worked as expected on my system (macOS BigSur 11.6 / R v4.1.1 / Rstudio v1.4.1717).

Given your blastn was successful, perhaps you are combining multiple fasta files for your protein fasta reference database? If that's the case, try concatenating them together and use the path to the file instead of an R object ("fa") when making your blastdb. Or perhaps:

Source https://stackoverflow.com/questions/69384247

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install rBLAST

Install the package devtools. Install the Bioconductor package Biostrings either using devtools::install_bioc("Biostrings") or directly from [Bioconductor](http://www.bioconductor.org/install/). Install rBlast from GitHub using devtools::install_github("mhahsler/rBLAST"). Install the BLAST software by following the instructions found in ? blast.
Install the package devtools.
Install the Bioconductor package Biostrings either using devtools::install_bioc("Biostrings") or directly from [Bioconductor](http://www.bioconductor.org/install/).
Install rBlast from GitHub using devtools::install_github("mhahsler/rBLAST").
Install the BLAST software by following the instructions found in ? blast

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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