hmmer | HMMER : biological sequence analysis using profile HMMs | Genomics library

by EddyRivasLab C Version: infernal-1.1.4 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(3)Vulnerabilities Install Support

kandi X-RAY | hmmer Summary

hmmer is a C library typically used in Artificial Intelligence, Genomics applications. hmmer has no bugs, it has no vulnerabilities and it has low support. However hmmer has a Non-SPDX License. You can download it from GitHub.

HMMER searches biological sequence databases for homologous sequences, using either single sequences or multiple sequence alignments as queries. HMMER implements a technology called "profile hidden Markov models" (profile HMMs). HMMER is used by many protein family domain databases and large-scale annotation pipelines, including Pfam and other members of the InterPro Consortium. To obtain HMMER releases, please visit hmmer.org. To participate in HMMER development, visit us at github. HMMER development depends on the Easel library, also at github.

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Quality

Security

License

Reuse

Support

hmmer has a low active ecosystem.

It has 238 star(s) with 63 fork(s). There are 14 watchers for this library.

It had no major release in the last 6 months.

There are 7 open issues and 241 have been closed. On average issues are closed in 152 days. There are 4 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of hmmer is infernal-1.1.4

Quality

hmmer has 0 bugs and 0 code smells.

Security

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

hmmer code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

hmmer has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

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

Installation instructions, examples and code snippets are available.

It has 563 lines of code, 14 functions and 3 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

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hmmer Key Features

No Key Features are available at this moment for hmmer.

hmmer Examples and Code Snippets

No Code Snippets are available at this moment for hmmer.

Community Discussions

Trending Discussions on hmmer

How do i create env from .yml file in conda in windows?

Convert a hmmer --tblout output to a pandas dataframe

Struggling with PDF output of bookdown

QUESTION

How do i create env from .yml file in conda in windows?

Asked 2020-Aug-03 at 00:49

I have just started using miniconda on windows and was creating an environment through a .yml file but got this error.

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ANSWER

Answered 2020-Aug-03 at 00:49

There are a couple of issues. First, going across platforms (linux-64 to win-64) is not directly supported. There are other answers that address this. Second, and more prohibitive, is that Bioconda does not support Windows and some of the packages (e.g., hmmer) are specifically from there.

Alternatives could be either building up the dependencies in Conda env, plus a compiler meta-package (compiler-cxx, make), then installing non-Windows software from source (e.g., see HMMER documentation); or running Conda under WSL.

Source https://stackoverflow.com/questions/63214608

QUESTION

Convert a hmmer --tblout output to a pandas dataframe

Asked 2020-May-27 at 14:44

Is there a way to convert a hmmer output to a pandas dataframe?
I am also unsure how to load a hmmer tblout table into python via the Bio module.

I believe you can call a hmmer format with SeqIO.parse or SeqIO.search.The format of the table appears tab separated however it seems to be a collection of random spaces meaning if I remove the headers and # leaving only the table information there is not easy way to split the table using a tab separator.

A small example of a hmmer --tblout file is below:

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ANSWER

Answered 2020-May-27 at 14:44

I would build a dictionary from the attributes you are interested in and make a DataFrame from that dictionary. Say you are interested in the attributes of the hits:

Source https://stackoverflow.com/questions/62012615

QUESTION

Struggling with PDF output of bookdown

Asked 2020-Feb-20 at 16:07

I thought it would be a good idea to write a longer report/protocol using bookdown since it's more comfortable to have one file per topic to write in instead of just one RMarkdown document with everything. Now I'm faced with the problem of sharing this document - the HTML looks best (except for wide tables being cut off) but is difficult to send via e-mail to a supervisor for example. I also can't expect anyone to be able to open the ePub format on their computer, so PDF would be the easiest choice. Now my problems:

My chapter headings are pretty long, which doesn't matter in HTML but they don't fit the page headers in the PDF document. In LaTeX I could define a short title for that, can I do that in bookdown as well?

I include figure files using knitr::include_graphics() inside of code chunks, so I generate the caption via the chunk options. For some figures, I can't avoid having an underscore in the caption, but that does not work out in LaTeX. Is there a way to escape the underscore that actually works (preferrably for HTML and PDF at the same time)? My LaTeX output looks like this after rendering:

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ANSWER

Answered 2020-Feb-20 at 16:07

Concerning shorter headings: pandoc, which is used for the markdown to LaTeX conversion, does not offer a "shorter heading". You can do that yourself, though:

Source https://stackoverflow.com/questions/60226866

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

Vulnerabilities

No vulnerabilities reported

Install hmmer

Executable programs will be installed in /your/install/path/bin. If you leave this optional ./configure argument off, the default prefix is /usr/local.
INSTALL - brief installation instructions.
Userguide.pdf - the HMMER User's Guide.

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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