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a python script to recognize specific sequence of tags
Tag-find is a python script developed to clean up reads from a specific 12 nucleotides long tag sequence used during the cDNA library preparation for RNA-seq experiments.
Tools for mapping RNA-Seq reads to eukaryotic genomes
Tuque includes 4 programs:
tuqueIndex to prepare Bowtie indexes that include spliced sequences
tuqueMap to map reads using the prepared indices
tuqueSplice to find splice junctions from the reads
tuqueCount to count the reads mapping within annotated sequence intervals
BoulderALE is an RNA alignment editor, which allows for the annotation of basepairs, annotation and collapsing of features (horizontal) and sequences (vertical), along with 2D display of sequences and base composition given a secondary structure.
Cloud data warehouse to power your data-driven innovation
BigQuery is a serverless and cost-effective enterprise data warehouse that works across clouds and scales with your data.
BigQuery Studio provides a single, unified interface for all data practitioners of various coding skills to simplify analytics workflows from data ingestion and preparation to data exploration and visualization to ML model creation and use. It also allows you to use simple SQL to access Vertex AI foundational models directly inside BigQuery for text processing tasks, such as sentiment analysis, entity extraction, and many more without having to deal with specialized models.
BARNACLE is a Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.
A colorized interactive dotplot program designed for pair-wise comparisons of RNA & DNA. The original idea was from the mind of late Prof. William J. Dreyer of Caltech. The idea is to be able to see the "tapestry" of life, which comes alive with color.
ParticleStats is software for analysing tracked particles from RNA Localization experiments. Analysis is performed on the X and Y coordinated of the tracked RNA particles
openSputnik is a robust distributed platform for massive scale precalculation of genetic and genomic data using contemporary bioinformatics methods. Annotated DNA, RNA and protein sequences are stored as binary objects in a variery of relational database
The RNA Ontology Consortium proposed a translation the RNA backbone angles to 46 clusters ('suites') and hence unique names. This project calculates the suites from RNA 3D structures, and to search on a Java-based index structure of known folds.
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