molbery 1.0.6

A tool for Molecular biologists to design modified Molecular Beacons which works on Exonuclease III Aided Target Recycling strategy for the detection of nucleic acid signatures.

MOLecular Beacons powered by ExonucleaseIII RecYcling.

Molbery is a python based tool which identifies 29mer probes with 7 bases in stem, 8 in loop and 7 overhang bases from a fasta sequence. This is based on the method developed by Zuo, Xiaolei, et al. [Ref1] which descibes an Exo III aided target recycling method for nucleic acid signature amplification. It uses the formula suggested by Howley, Peter M., et al. [Ref2] for calculation of melting temperature of the probes. Other than general criteria like GC content & Tm, there are special considerations in the property of the probe sequence which are reported to be optimal. More information will be available after publication of the tool in a scientific journal.

Features

The latest release includes:

Support for Fasta & multi-Fasta format

Manual specification of GC content, Tm range & Salt Conc.

reStructuredText Output

BLAST connect with parallel execution

Compatibility

Molbery is a cross platform tool which runs on Windows, Linux and OS X with the latest & major releases of python 2 & 3.

License

Molbery is an open source tool available under the OSI approved MIT license.

Copyright (c) 2016 Bhagya C T

Copyright (c) 2016 Manu S

Please read the license content here.

Installation

All the Python packages required for Molbery will be installed with pip.

Run cmd with Administrator permissions in Windows.

> pip install molbery

Run command with sudo permissions in Linux and OS X.

$ sudo pip install molbery

You can manually download the Molbery repository or simply clone it.

$ git clone https://github.com/bhagya-ct/molbery

Usage

After succesful installation refer command help for all available options.

$ molbery --help

For a single FASTA input run

$ molbery <path_to_fasta> --blast --out <output> -g <GC_min> -c <GC_max> -t <Tm_min> -m <Tm_max> -s <salt_conc_in_molar_units>

For a multi-FASTA input run (Output cannot be specified for multiple seq. Default is sequence ID present in multi-FASTA)

$ molbery <path_to_fasta> --blast --multi -g <GC_min> -c <GC_max> -t <Tm_min> -m <Tm_max> -s <salt_conc_in_molar_units>

Sample Output

Sequence ID - <gid_of_sequence>

Probe	Molberys (29mer Probes)	GC (%)	Tm (C)	Stem Tm (C)	Loop Tm (C)
1	ACCGTAGAGCTACGACTACGGTACATTAC	48.28	69.9	22	24
2	AGTCGTATGCATACGTACGACTAAGCTAC	44.83	68.9	20	24
3	ACTTTTCGTGCTGAAGAAAAGTGAAAGCG	41.38	66.9	18	24
4	AGCTTAGACGTACGACTAAGCTACGACTA	44.83	68.9	20	24
5	AGATTCGAAGCGAACCGAATCTGCATACG	48.28	69.9	20	24

Note: Blast Outputs are written to <Output>_blast_results/ folder with individual text file for every probe.

Authors and Contributors

The tool is designed and developed by Bhagya C T, Scientist-Biotechnology, Omix Research & Diagnostics Labs and Manu S, Institute of Bioinformatics & Applied Biotechnology. The authors are grateful to Dr. Sudeshna Adak, CEO & Director, Omix Research & Diagnostics Labs for providing important technical supervision and discussions.

Source code

The source codes of Molbery are available

via git: https://github.com/bhagya-ct/molbery

via Pypi: https://pypi.python.org/pypi/molbery

Credits

Thanks to the Pythonistas for some wonderful plugin modules and libraries which saves a lot of Caffeine and Code!

• joblib

• argparse

• tabulate

• regex

• biopython

FAQs

Q1) pip command not found?

Ans. You probably don’t have the latest release of Python. Update Python or install pip.

Q2) Installation was successful but could not find molbery command?

Ans. You would not have given Admin or sudo permissions while installing. Run $ pip uninstall molbery and reinstall with Admin or sudo permissions.

Bugs

If you find a bug in molbery (pypi), please try to reproduce it with latest python 2.7 and 3.5.

If the problem persists, please file a bug in the github issue tracking system in the repository page. For questions, troubleshooting and requests, please feel free to contact us at [e-mail] or [e-mail]

References

[Ref1]

Zuo, X., Xia, F., Xiao, Y., & Plaxco, K. W. (2010). Sensitive and selective amplified fluorescence DNA detection based on exonuclease III-aided target recycling. Journal of the American Chemical Society, 132(6), 1816-1818.

[Ref2]

Howley, P. M., Israel, M. A., Law, M. F., & Martin, M. A. (1979). A rapid method for detecting and mapping homology between heterologous DNAs. Evaluation of polyomavirus genomes. Journal of Biological Chemistry, 254(11), 4876-4883.