CATSNAP
CATSNAP (Conserved AlTernative SpliciNg in Animals and Plants) is an algorithmic pipeline for assessing the conservation of putative protein isoforms generated by alternative splicing. It employs a machine learning approach following a database search with the provided pair of protein sequences.
Availability
Citation
Timofeyenko K, Kanavalau D, Alexiou P, Kalyna M, Růžička K (2023) Catsnap: a user-friendly algorithm for determining the conservation of protein variants reveals extensive parallelisms in the evolution of alternative splicing. New Phytologist, 238: 1722-1732. DOI: 10.1111/nph.18799
Tobacco cell line BY-2 (N. tabacum L. cv Bright Yellow 2) transcriptomic data
Seven biological replicates of Nicotiana tabacum L. cv. Bright Yellow (BY-2) cell culture samples cultured at auxin supplemented conditions (ctrl) and three replicates of BY-2 cell culture samples cultured at auxin-starved (AF) conditions. Samples collected 48 hours after culture inoculation.
Availability
Rough sequencing data are available through GEO Series accession number GSE160438 at the Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/).
Citation
Müller K, Dobrev PI, Pěnčík A, Hošek P, Vondráková Z, Filepová R, Malínská K, Brunoni F, Helusová L, Moravec T, Retzer K, Harant K, Novák O, Hoyerová K, Petrášek J (2021) DIOXYGENASE FOR AUXIN OXIDATION 1 catalyzes the oxidation of IAA amino acid conjugates. Plant Physiology, 187(1): 103-115, DOI: 10.1093/plphys/kiab242