aptamerutils

Introduction

aptamerutils is a simple Python package for short nucleic acid sequences (for example, aptamers) arrangement, sorting, clustering.

This package can be installed from PyPI:

pip install aptamerutils

For more about classes and functions of this package, see notebook files in .docs/.

Example

This is a figure of aptamer clustering result. .pdf, .png, .svg files are all supported as output. The colored bases are feature fragments of each cluster (family), as the bolded bases are unpaired predicted by Viennarna when a nucleic acid molecule forms its secondary structure.

versions

0.1.0

• Initial release
• Clustering of short nucleic acid sequences
• Search desired nucleic acid sequences (logical operations supported)

0.2.0

• Webapp for clustering is developed
• Fuzzy matching is supported when trimming
• Kmer library of a SeqList object can be directly extracted

0.3.0

• Output figure is shown can be shown in a different way, now it is more similar to a clustering result published in a paper of aptamers. Style in 0.1.0 -- 0.2.0 is also preserved
• Fuzzy matching is added to webapp
• Suspicious sequences ( contain characters other than ATCGU ) in a SeqList object will be deleted when trimming