Home

• Introduction
• Genome assemblies
• Manual
• Walkthrough
• Toy examples
• Validation
• The (official) Manna song
• piRNAclusterComparison

Introduction

Welcome to Manna, a novel tool to align multiple sequences of annotations (e.g. RepeatMasker annotations of piRNA clusters).

Genome assemblies

We generated long-read assemblies of two D. simulans lines (SZ232 and SZ45): https://sourceforge.net/projects/manna/files/assemblies/

(for completeness, other assemblies used in this work: https://sourceforge.net/projects/manna/files/assemblies/previously_published-assemblies/)

Manual

Please consult the [Manual] for explanation of the core script.

Walkthrough

A [Walkthrough] is available using piRNA cluster 42AB from 5 D. melanogaster lines

Toy examples

Several evolutionary scenarios are shown in [Toy examples].

Validation

• [validation_fixed] A simple scenario - just fixed TE insertions for all families in Drosophila. Also an introduction to our validation approach, so please read this first if you interested in the validations.
• [validation_fix_seg] Alternating fixed and segregating insertions for all TE families in Drosophila
• [validation_msms] Neutral site frequency spectrum of TE insertions
• [validation_linearlandscape] for publication; random population frequency of TE insertions with N=5; one of the individuals has an insertion of each TE segregating in the population, thus providing a backbone
• [validation_mixfamfreq] for publication; random popualtion frequency of families (families and NOT insertions as before) with N=5

The (official) Manna song

Finally the (official) Manna song https://www.youtube.com/watch?v=8N_tupPBtWQ&ab_channel=VeselinTrayanov

piRNAclusterComparison

Complementarily to Manna, we can also visualize the comparision of piRNA cluster with EasyFig, which uses the similarity between the aligned sequences and the TE annoations.
Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011 Apr 1;27(7):1009-10. doi: 10.1093/bioinformatics/btr039. Epub 2011 Jan 28. PMID: 21278367; PMCID: PMC3065679.

A walkthrough for this visualization with cluster 38C for three D. melanogaster strains can be found here [piRNAclusterComparison-walkthrough].
Although EasyFig supports comparisons of multiple sequences, this feature can solely display the feature labels (e.g. the TE names) of the first and the last assembly. To prevent loss of feature labels for the intermediate assemblies, we perform pairwise comparisions and then combine them.
Additionally, we modified the originial EasyFig script to write labels in a monospaced font (consolas) and to set the blastn similiarity to a fixed range between 70%-100% which enables us to compare the individually generated plots.
We are thus able to visualize comparisons of clusters from multiple assemblies (currently, up to 9 assemblies).
Note that currently several parameters are hardcoded in this pipeline (e.g. color D. melanogaster TEs by orders or a miminium blastn similarity block of 3 kb).

Project Members:

• Filip Wierzbicki (admin)
• Robert Kofler (admin)
• Sarah Signor (admin)