International Multiconference “Bioinformatics of Genome Regulation and Structure\Systems Biology”

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pipeline

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Genomics, transcriptomics, bioinformatics symposiumRTrans: a pipeline for multi-way analysis of differential gene expression profiles

RTrans: a pipeline for multi-way analysis of differential gene expression profiles

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Poster (download)

[pdf-embedder url=”https://bgrssb.icgbio.ru/wp-content/uploads/2020/07/257.pdf”]
George Sergeevich Krasnov1, Anastasiya Andreevna Kobelyatskaya2, Anastasiya Vladimirovna Snezhkina3, Vladislav Sergeevich Pavlov4, Elena Anatolevna Pudova5, Anna Victorovna Kudryavtseva6
1EIMB RAS, gskrasnov@mail.ru
2EIMB RAS, kaa.chel@mail.ru
3EIMB RAS, leftger@rambler.ru
4EIMB RAS, vladislav1pavlov@gmail.com
5EIMB RAS, pudova_elena@inbox.ru
6EIMB RAS, rhizamoeba@mail.ru

RNA-Seq is a widespread technique routinely used to reveal differentially expressed (DE) genes, splicing events and affected signaling pathways. Usually, RNA-Seq data analysis needs skills in programming and bioinformatics. We aimed at developing easy-to-use pipeline covering multiple aspects of DE analysis. Here we present RTrans pipeline aimed at evaluating differential gene expression, pathway enrichment, WGCNA co-expression analysis and visualization. It provides rapid analysis of read counts data including MANOVA, paired tests, non-parametric tests. RTrans represents a versatile pipeline facilitating DE analysis based on RNA-Seq and other quantitative data.

Genomics, transcriptomics, bioinformatics symposiumAutomatic Annotation of Operons Responsible for O-antigen Synthesis

Automatic Annotation of Operons Responsible for O-antigen Synthesis

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Danil Zilov1, Polina Chesnokova2, Alexey Komissarov3
1Laboratory of Applied Genomics, SCAMT, ITMO University, St. Petersburg, Russia, zilov@scamt-itmo.ru
2Laboratory of Applied Genomics, SCAMT, ITMO University, St. Petersburg, Russia, chesnokova@scamt-itmo.ru
3Laboratory of Applied Genomics, SCAMT, ITMO University, St. Petersburg, Russia, komissarov@scamt-itmo.ru

Unfortunately, the most ready-made tools for serotype determination are limited to genome E. Coli only. However, there is a problem due to the low accuracy of Рћ-antigen cluster identification in the genome. Pipeline, which was created due the work, solves this problem and can be used to find and annotate a cluster of genes in genome of the most gram-negative bacteria.