Functional Analysis of Newly Sequenced Species with Blast2GO Carlos Menor, David Seide, Robert Nica, Mariana Monteiro, Alejandro Rocamonde, Francisco Salavert, Stefan Götz BioBam S.L., Valencia, Spain

Abstract Toolbox features

RNA-seq Features: attempts to describe functions of genes and Quality assessment, trimming, assembly, quantification, pair- by making use of data derived from genomic and filtering and adapter removal of wise and time-course transcriptomic experiments. raw sequence data differential expressions analysis Blast2GO is a bioinformatics platform which offers an integrated solution for functional genomics analysis of novel genomes. It allows biologists to get from raw NGS data through all steps up to the Eukaryotic and prokaryotic High-throughput functional generation of biological insights for a species without any previous genome characterization annotation prediction genome resources. supported by RNA-seq data

This poster provides an overview of the different analysis strategies, details about new features as well as describes the bioinformatic Rich Visualization: Functional enrichment and pipeline of a de-novo transcriptomics analysis - from read-assembly up Track-based genome browser for pathway analysis to the functional analysis and generation of biological insights. GFF, VCF, BAM and FASTA files

1. Quality check and pre-processing Complete Transcriptome 3. Expression quantification and raw sequence data Analysis Workflow differential expression analysis

A good quality control check and preprocessing Blast2GO provides a fast and easy way to of raw sequence data coming from high quantify transcript expression levels from RNA- throughput sequencing pipelines is fundamental Seq data and to perform differential expression for optimal downstream analysis. Blast2GO analysis to detect significantly expressed provides summary evaluations that guide the transcripts. Pair-wise comparisons as well as preprocessing of libraries, which includes time-course analysis can be conducted. adapters removal, trimming and filtering of low quality reads.

2. De novo transcript reconstruction and functional characterization 4. Functional Enrichment Analysis

Blast2GO allows to reconstruct the By combining differential expression results transcriptome by assembling RNA sequencing with functional annotations, enrichment reads into contigs without the use of a analysis can be carried out using two different reference genome. The resulting transcripts can methods: Fisher’s Exact Test and GSEA. be evaluated and characterized taking Blast2GO can identify functions that are over- advantage of different functionalities: Blast, represented in a group of transcripts. The GO Annotation, InterProScan, Coding Potential interpretation of results allows to gain a better Assessment, KEGG Pathways, RFAM, EggNOG, understanding of the underlying biological etc. processes.

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