Search Results for "biopython"
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Showing 6 open source projects for "biopython"
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Python4Proteomics Course
Python course for Proteomics analysis
Python course (in Spanish) for Proteomics analysis using basically Jupyter NoteBooks. For more information, you can have a look at the readme.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/p4p/code/ci/default/tree/readme.md -
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UniPyRange
Tool to fetch protein/DNA truncation constructs from Uniprot DB
...Lets say you want the amino acid sequence of range 128-387 from a 1000 amino acid protein - this script will help you to avoid counting mistakes by just showing you the specified sequence in amino acids and coding DNA base pairs (ideal for amplification primer design) of a specified Uniprot ID. - Requires BioPython (3) and Bioservices Package (4) (1) The UniProt Consortium UniProt: a hub for protein information Nucleic Acids Res. 43: D204-D212 (2015). (2) RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014 Jan 1;42(1):D756-63. (3) Cock PJ et al. Bioinformatics (2009) (4) Cokelaer et al, Bioinformatics (2013) -
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reciprocal blast for windows
Pipeline for automatic reciprocal blast
Set of python3 scripts and windows batch scripts which use extensively NCBI Blast+ package and BioPython module to perform algorithm known as reciprocal blast. README: https://sourceforge.net/projects/reciprocalblastwin32/files/ -
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We developed a universal approach and tool designated Geptop, based on orthology and phylogeny, to offer gene essentiality annotations. The web server and standalone version of Geptop are available at http://cefg.uestc.edu.cn/geptop/ free of charge. This package is dependent on Python, Biopython and BLAST+. Citation: Wei W, Ning L-W, Ye Y-N, Guo F-B (2013) Geptop: A Gene Essentiality Prediction Tool for Sequenced Bacterial Genomes Based on Orthology and Phylogeny. PLoS ONE 8(8): e72343. doi:10.1371/journal.pone.0072343
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Bioinformatic C++ library providing a central engine to other bio* libraries (BioPerl, BioPython, BioJava).
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Ducking is a software who is providing simulation of probable docking between two proteins using rigid body monte carlo method. It is written in python and uses the libraries wxPython, VTK, SciPy and BioPython.
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