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prrn5 gene structure aware alignment scripts

posted on 2022-01-08, 02:56 authored by David Stern, Clair HanClair Han
Code for generating gene-structure aware sequence alignments for intron position comparison, from publication "Gene structure-based homology search identifies highly divergent putative effector gene family", Stern and Han,

Intron concordance analysis for all species plotted in publication:
Intron_alignments_v5.5.6.Rmd generates figure panels S5, S7C, S8, S10D-F, S11A.
Input extended FASTA files generated in their respective species analysis scripts, available on Janelia Figshare at https://doi.org/10.25378/janelia.17868413

Background intron concordance analysis using randomly chosen ortholog groups:
classifier_orthogroup_Hcor_repeated_sampling.Rmd generates figure S6.
Input extended FASTA files generated in classifier_orthogroup_Hcor.Rmd, using "Augustus.updated_w_annots.3ix21_final.pep_longest__v__Apis.Augustus.updated_w_annots.7vii21.pep_longest.tsv" as input.

Please contact Clair Han at hanc@janelia.hhmi.org with questions.

See related materials in collection at https://doi.org/10.25378/janelia.c.5778905.