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Compare sequence similarity of mature miRNA across species and with database matches #45

Closed sr320 closed 5 months ago

sr320 commented 6 months ago

Create a cladogram / PCA etc that shows grouping of mature miRNAs of three species with those matches in the database.

sr320 commented 6 months ago

possible programs.

For aligning short miRNA sequences and generating visualizations in R, you might consider the following packages:

Biostrings - This package from Bioconductor is excellent for handling biological sequences. It provides functions for reading, manipulating, and aligning short sequences, which is ideal for miRNA.

ShortRead - Also from Bioconductor, this package is tailored for handling high-throughput sequencing data, including short sequences like miRNAs. It includes functionality for quality assessment, alignments, and data visualization.

Gviz - For visualization, Gviz (from Bioconductor) is a great choice. It is designed for visualizing genomic data and can be very useful for displaying the results of miRNA alignments in a genomic context.

sr320 commented 6 months ago

Note Need to include database hits too....

Can you provide links to mature miRNAs fastas for all three species. (3 files is fine) Fasta file with database matches.

sr320 commented 6 months ago

Another maybe more feasible: for every mature miRNA provide the score and evalue for top hit in each of two other species.

(be sure to use short rna flag)

shedurkin commented 6 months ago

Can you provide links to mature miRNAs fastas for all three species. (3 files is fine) Fasta file with database matches.

https://github.com/urol-e5/deep-dive/blob/main/DEF-cross-species/output/10-shortRNA-ShortStack-comparison/Apul_results_mature.txt https://github.com/urol-e5/deep-dive/blob/main/DEF-cross-species/output/10-shortRNA-ShortStack-comparison/Peve_results_mature.txt https://github.com/urol-e5/deep-dive/blob/main/DEF-cross-species/output/10-shortRNA-ShortStack-comparison/Pmea_results_mature.txt

sr320 commented 6 months ago

Fastas, those are not fastas...

shedurkin commented 6 months ago

oops, here you go

Apul: https://github.com/urol-e5/deep-dive/blob/main/DEF-cross-species/output/10-shortRNA-ShortStack-comparison/Apul_ShortStack_mature_annotated.fasta

Peve: https://github.com/urol-e5/deep-dive/blob/main/DEF-cross-species/output/10-shortRNA-ShortStack-comparison/Peve_ShortStack_mature_annotated.fasta

Pmea: https://github.com/urol-e5/deep-dive/blob/main/DEF-cross-species/output/10-shortRNA-ShortStack-comparison/Pmea_ShortStack_mature_annotated.fasta

shedurkin commented 6 months ago

completed, code rendered and pushed (https://github.com/urol-e5/deep-dive/blob/main/DEF-cross-species/code/10-shortRNA-ShortStack-comparison.md).

sr320 commented 6 months ago

Lets still do this

for every mature miRNA provide the score and evalue for top hit in each of two other species.

shedurkin commented 5 months ago

https://github.com/urol-e5/deep-dive/blob/main/DEF-cross-species/output/10-shortRNA-ShortStack-comparison/combined_blast.tab Table of top blastn hits in each species for all individuals