Karolis Ramanauskas
University of Illinois at Chicago
Department of Biological Sciences
840 W. Taylor St.
SEL 4093 M/C 067
Chicago, IL 60607
E-Mail: kraman2@uic.edu

I am a graduate student in the Igić lab at the University of Illinois at Chicago. I study mating system evolution in flowering plants.

More specifically, I am interested in the molecular evolution and genetic architecture of the S-ribonuclease-based mechanism of self-incompatibility found in many angiosperms. It is unclear whether this mechanism originated once and this homology is retained across eudicots, or if its components were re-recruited independently.

kakapo: Extract and annotate genes from raw RNA-seq reads

Studies in many fields within life sciences increasingly rely on RNA sequencing (RNA-seq) data. As a result, RNA-seq datasets deposited to the NCBI Sequence Read Archive (SRA) are proliferating. In addition to serving as an archive for the original studies, these datasets present an opportunity for novel research. Kakapo allows users to extract and assemble a specified gene or protein family from any number of SRA accessions (or their own RNA-seq data). Kakapo identifies open reading frames in the assembled transcripts and annotates them using InterProScan. Additionally, raw reads can be filtered for ribosomal, plastid, and mitochondrial reads or reads belonging to non-target organisms (viral, bacterial, etc.)

Available on GitHub

My talk about the kakapo pipeline presented at the Botany 2020 conference: YouTube

Service for the Phylogenetic Placement of T2/S-RNases

This web service aims to enable and ease the phylogenetic placement and classification of new T2/S-type RNases. It arises out of our lab's previously published papers^1,2. Please read Ramanauskas and Igić 2017² for details underpinning the starting trees and rationale for analyses.